Analyses for Publication
AGC
2023-09-27
Last updated: 2026-03-18
Checks: 7 0
Knit directory: scSeq_Hefendehl/
This reproducible R Markdown analysis was created with workflowr (version 1.7.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20260317) was run prior to running
the code in the R Markdown file. Setting a seed ensures that any results
that rely on randomness, e.g. subsampling or permutations, are
reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 05a87a1. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish or
wflow_git_commit). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: output/All_genes_Clusters.svg
Ignored: output/All_genes_Clusters_byCondition.svg
Ignored: output/All_genes_Clusters_byHomeostatgenes.svg
Ignored: output/All_genes_Clustertree.svg
Ignored: output/CClustering_CellPhase.svg
Ignored: output/CClustering_CellPhaseG2MScore.svg
Ignored: output/CClustering_CellPhaseG2MScoreViolin.svg
Ignored: output/CClustering_CellPhaseScore.svg
Ignored: output/CClustering_CellPhaseScoreViolin.svg
Ignored: output/Cellcount_distribution_MouseByCluster.xlsx
Ignored: output/Cellcount_distribution_MouseBygenotype.xlsx
Ignored: output/Celltypes_Opt_All_genes_all_cells_Clusters.svg
Ignored: output/Celltypes_Opt_All_genes_all_cells_Clusters_byCondition.svg
Ignored: output/Celltypes_Opt_All_genes_all_cells_Clusters_byPlate.svg
Ignored: output/Cluster_distribution_genotype.xlsx
Ignored: output/Clusters_GOterms_Markers_all.xlsx
Ignored: output/Clusters_Markers_all.xlsx
Ignored: output/CrossFCplot.pdf
Ignored: output/CrossFCplot.svg
Ignored: output/DEG_GO_plotsMicroglia2vsMicroglia4.svg
Ignored: output/DEG_GO_plotsMicroglia2vsMicroglia4_comorbid.svg
Ignored: output/DEG_GO_plotsMicroglia3vsMicroglia2.svg
Ignored: output/DEG_GO_plotsMicroglia3vsMicroglia2_comorbid.svg
Ignored: output/DEG_GO_plotsMicroglia5vsMicroglia0.svg
Ignored: output/DEG_GO_plotsMicroglia5vsMicroglia0_comorbid.svg
Ignored: output/DEG_GO_plotsMicroglia5vsMicroglia6.svg
Ignored: output/DEG_GO_plotsMicroglia5vsMicroglia6_comorbid.svg
Ignored: output/DEG_GO_plotsMicroglia6vsMicroglia0.svg
Ignored: output/DEG_GO_plotsMicroglia6vsMicroglia0_comorbid.svg
Ignored: output/DEG_Genelist_Microglia2vsMicroglia4.xlsx
Ignored: output/DEG_Genelist_Microglia2vsMicroglia4_comorbid.xlsx
Ignored: output/DEG_Genelist_Microglia3vsMicroglia2.xlsx
Ignored: output/DEG_Genelist_Microglia3vsMicroglia2_comorbid.xlsx
Ignored: output/DEG_Genelist_Microglia5vsMicroglia0.xlsx
Ignored: output/DEG_Genelist_Microglia5vsMicroglia0_comorbid.xlsx
Ignored: output/DEG_Genelist_Microglia5vsMicroglia6.xlsx
Ignored: output/DEG_Genelist_Microglia5vsMicroglia6_comorbid.xlsx
Ignored: output/DEG_Genelist_Microglia6vsMicroglia0.xlsx
Ignored: output/DEG_Genelist_Microglia6vsMicroglia0_comorbid.xlsx
Ignored: output/DEG_Vulcano_Microglia2vsMicroglia4.svg
Ignored: output/DEG_Vulcano_Microglia2vsMicroglia4_comorbid.svg
Ignored: output/DEG_Vulcano_Microglia3vsMicroglia2.svg
Ignored: output/DEG_Vulcano_Microglia3vsMicroglia2_comorbid.svg
Ignored: output/DEG_Vulcano_Microglia5vsMicroglia0.svg
Ignored: output/DEG_Vulcano_Microglia5vsMicroglia0_comorbid.svg
Ignored: output/DEG_Vulcano_Microglia5vsMicroglia6.svg
Ignored: output/DEG_Vulcano_Microglia5vsMicroglia6_comorbid.svg
Ignored: output/DEG_Vulcano_Microglia6vsMicroglia0.svg
Ignored: output/DEG_Vulcano_Microglia6vsMicroglia0_comorbid.svg
Ignored: output/Ellbowplot.svg
Ignored: output/G2M_Opt_All_genes_all_cells_Clusters.svg
Ignored: output/G2M_Opt_All_genes_all_cells_Clusters_byCondition.svg
Ignored: output/G2M_Opt_All_genes_all_cells_Clusters_byPlate.svg
Ignored: output/Gene_list_based_Clusters.svg
Ignored: output/Gene_list_based_Clusters_byCondition.svg
Ignored: output/Gene_list_based_Clusters_byHomeostatgenes.svg
Ignored: output/Gene_list_based_Clustertree.svg
Ignored: output/MGscores_FeatMaps.svg
Ignored: output/MGscores_RidgePlots.svg
Ignored: output/Microgila_WGCNA_Eigenscore.svg
Ignored: output/Microgila_WGCNA_Eigenscore_byCluster.svg
Ignored: output/Microglia_DAM1_binary.svg
Ignored: output/Microglia_DAM1_bygenotype.svg
Ignored: output/Microglia_DAM1_calling.svg
Ignored: output/Microglia_DAM1_scoring.svg
Ignored: output/Microglia_DAM1_thresholding.svg
Ignored: output/Microglia_DAM2_bygenotype.svg
Ignored: output/Microglia_DAM2_calling.svg
Ignored: output/Microglia_DAM2proportionsofDAM1_per_condition.svg
Ignored: output/Microglia_DAM2proportionsofDAM1_per_condition_APPPS1.svg
Ignored: output/Microglia_DAM2proportionsofDAM1_per_condition_WT.svg
Ignored: output/Microglia_DAMproportions_per_condition_APPPS1.svg
Ignored: output/Microglia_DAMproportions_per_condition_WT.svg
Ignored: output/Microglia_DAMproportions_per_condition_all.svg
Ignored: output/Microglia_DAMvsDAM2_contourplot.svg
Ignored: output/Microglia_DAMvsHomeo.svg
Ignored: output/Microglia_Dotplot_ClsuterCondition_Genelists.svg
Ignored: output/Microglia_Dotplot_Up_spatial_and_APPPS1vsAPPPS1stroke.svg
Ignored: output/Microglia_Dotplot_test.svg
Ignored: output/Microglia_HomeoDAMproportions_per_ckuster.svg
Ignored: output/Microglia_HomeoDAMproportions_per_condition.svg
Ignored: output/Microglia_HomeoDAMproportions_per_gender.svg
Ignored: output/Microglia_Homeo_DAM.svg
Ignored: output/Microglia_Homeo_binary.svg
Ignored: output/Microglia_Homeo_bygenotype.svg
Ignored: output/Microglia_Homeo_calling.svg
Ignored: output/Microglia_Homeo_scoring.svg
Ignored: output/Microglia_Homeo_thresholding.svg
Ignored: output/Microglia_Homeoproportions_per_condition.svg
Ignored: output/Microglia_Homeoproportions_per_condition_APPPS1.svg
Ignored: output/Microglia_Homeoproportions_per_condition_WT.svg
Ignored: output/Microglia_HomeostatGenes_Cluster_Ridgeplot.svg
Ignored: output/Microglia_HomeostatGenes_Featureplot.svg
Ignored: output/Microglia_Opt_All_genes_Aif1neg.svg
Ignored: output/Microglia_Opt_All_genes_Clusters.svg
Ignored: output/Microglia_Opt_All_genes_Clusters_byCondition.svg
Ignored: output/Microglia_Opt_All_genes_Clusters_byPlate.svg
Ignored: output/Microglia_Opt_All_genes_Condition.svg
Ignored: output/Microglia_Opt_All_genes_Gender.svg
Ignored: output/Microglia_Opt_All_genes_Immgen_sc_labels_agc.svg
Ignored: output/Microglia_Opt_All_genes_methoxy.svg
Ignored: output/Microglia_Opt_all_genes_AddGenelist.svg
Ignored: output/Microglia_Opt_all_genes_MicrogliaGenes.svg
Ignored: output/Microglia_Opt_all_genes_MicrogliaGenesRidgePlot.svg
Ignored: output/Microglia_Volcano_APPPS1CtrlvsAPPPS1Stroke.svg
Ignored: output/Microglia_Volcano_WTCtrlvsAPPPS1ctrl.svg
Ignored: output/Microglia_Volcano_WTCtrlvsWTStroke.svg
Ignored: output/Microglia_Volcano_WTstrokevsAPPPS1StrokeDAMgenes.svg
Ignored: output/Microglia_WGCNA_Dendrocolplot.svg
Ignored: output/Microglia_celltype_labels.svg
Ignored: output/Microglia_logFCCtrlvsStroke_APPPS1vsWT_all.svg
Ignored: output/Microglia_logFCCtrlvsStroke_APPPS1vsWT_sig_only.svg
Ignored: output/Microglia_mex.svg
Ignored: output/Opt_All_genes_all_cells_Clusters.svg
Ignored: output/Opt_All_genes_all_cells_Clusters_byCondition.svg
Ignored: output/Opt_All_genes_all_cells_Clusters_byPlate.svg
Ignored: output/Pseudotime1.svg
Ignored: output/Pseudotime1_Start4.svg
Ignored: output/Pseudotime1_Top10up_down_reg_Genes-correct.svg
Ignored: output/Pseudotime1_Top10up_down_reg_Genes-correct_Start4.svg
Ignored: output/Pseudotime1_genes.xlsx
Ignored: output/Pseudotime2.svg
Ignored: output/Pseudotime2Start4.svg
Ignored: output/Pseudotime2_Top10up_down_reg_Genes.svg
Ignored: output/Pseudotime2_Top10up_down_reg_GenesStart4.svg
Ignored: output/Pseudotime2_genes.xlsx
Ignored: output/Pseudotime3.svg
Ignored: output/Pseudotime3Start4.svg
Ignored: output/Pseudotime3_Top10up_down_reg_Genes.svg
Ignored: output/Pseudotime3_genes.xlsx
Ignored: output/Pseudotime_linages.pdf
Ignored: output/Pseudotime_linages.svg
Ignored: output/Pseudotime_linages_Start4.pdf
Ignored: output/Pseudotime_linages_Start4.svg
Ignored: output/Pseudotime_linages_startDAM.pdf
Ignored: output/Pseudotime_linages_startDAM.svg
Ignored: output/Qualityplots.svg
Ignored: output/Res_202602/
Ignored: output/Ridge_Custom_Genes.svg
Ignored: output/SeuratObjectafterProcessing.rds
Ignored: output/Top10GenesByExpr_Microglia0_Heatmaps_byCluster.svg
Ignored: output/Top10GenesByExpr_Microglia1_Heatmaps_byCluster.svg
Ignored: output/Top10GenesByExpr_Microglia2_Heatmaps_byCluster.svg
Ignored: output/Top10GenesByExpr_Microglia3_Heatmaps_byCluster.svg
Ignored: output/Top10GenesByExpr_Microglia4_Heatmaps_byCluster.svg
Ignored: output/Top10GenesByExpr_Microglia5_Heatmaps_byCluster.svg
Ignored: output/Top10GenesByExpr_Microglia6_Heatmaps_byCluster.svg
Ignored: output/Top10GenesByExpr_Microglia7_Heatmaps_byCluster.svg
Ignored: output/Top10Genes_Heatmaps_byCluster.svg
Ignored: output/WGCNAGeneWise_ExpressionModuleblue.svg
Ignored: output/WGCNAGeneWise_ExpressionModulebrown.svg
Ignored: output/WGCNAGeneWise_ExpressionModulegreen.svg
Ignored: output/WGCNAGeneWise_ExpressionModuleturquoise.svg
Ignored: output/WGCNAGeneWise_ExpressionModuleyellow.svg
Ignored: output/WGCNA_GO_terms.csv
Ignored: output/WGCNA_GO_terms.svg
Ignored: output/WGCNA_GO_terms.xlsx
Ignored: output/WGCNA_LinModStat_ByCluster.xlsx
Ignored: output/WGCNA_LinModStat_GTxTreatm.xlsx
Ignored: output/WGCNA_Module_Heatmaps.svg
Ignored: output/WGCNA_Module_Heatmaps_byCluster.svg
Ignored: output/WGCNA_Module_blue_Heatmaps_byCluster.svg
Ignored: output/WGCNA_Module_blue_allgenes_Heatmaps.svg
Ignored: output/WGCNA_Module_brown_Heatmaps_byCluster.svg
Ignored: output/WGCNA_Module_brown_allgenes_Heatmaps.svg
Ignored: output/WGCNA_Module_green_Heatmaps_byCluster.svg
Ignored: output/WGCNA_Module_green_allgenes_Heatmaps.svg
Ignored: output/WGCNA_Module_grey_Heatmaps_byCluster.svg
Ignored: output/WGCNA_Module_grey_allgenes_Heatmaps.svg
Ignored: output/WGCNA_Module_turquoise_Heatmaps_byCluster.svg
Ignored: output/WGCNA_Module_turquoise_allgenes_Heatmaps.svg
Ignored: output/WGCNA_Module_yellow_Heatmaps_byCluster.svg
Ignored: output/WGCNA_Module_yellow_allgenes_Heatmaps.svg
Ignored: output/WGCNA_brownselectedgenes_heatmap.svg
Ignored: output/WGCNA_brownselectedgenes_heatmap_byCluster.svg
Ignored: output/WGCNA_greenselectedgenes_heatmap.svg
Ignored: output/WGCNA_greenselectedgenes_heatmap_byCluster.svg
Ignored: output/WGCNA_greyselectedgenes_heatmap.svg
Ignored: output/WGCNA_greyselectedgenes_heatmap_byCluster.svg
Ignored: output/WGCNA_labeled_Heatmap.svg
Ignored: output/WGCNA_labeled_Heatmap_byCluster.svg
Ignored: output/WGCNA_turqouiseselectedgenes_heatmap.svg
Ignored: output/WGCNA_turqouiseselectedgenes_heatmap_byCluster.svg
Ignored: output/archive/
Ignored: output/cluster_desiree_orginal.pdf
Ignored: output/cluster_desiree_orginalXIST.pdf
Ignored: output/geneInfoSigned.csv
Ignored: output/net.rds
Ignored: output/powertable.rds
Untracked files:
Untracked: ConsensusTOM-block.1.rda
Untracked: analysis/archive/
Untracked: data
Untracked: shinySecret.R
Unstaged changes:
Deleted: analysis/00.1_Original_Analysis_Integrated.Rmd
Deleted: analysis/00_Original_Analysis.Rmd
Deleted: analysis/01_Biostat.Rmd
Deleted: analysis/02_plotsforPub.Rmd
Deleted: analysis/03_New_AnalysesforPub.Rmd
Deleted: analysis/03_New_AnalysesforPub_StateOct2025.Rmd
Deleted: analysis/04_plotsforPub.Rmd
Deleted: analysis/05_AnalysesforPub_202602.Rmd
Deleted: data/README.md
Modified: wflowhelper.R
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were
made to the R Markdown
(analysis/scRNA_Analyses_Candlishetal.Rmd) and HTML
(docs/scRNA_Analyses_Candlishetal.html) files. If you’ve
configured a remote Git repository (see ?wflow_git_remote),
click on the hyperlinks in the table below to view the files as they
were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 05a87a1 | achiocch | 2026-03-18 | workflowr::wflow_publish(c("./analysis/sc", "./analysis/index")) |
load second batch
metadata additional samples
load additonal samples second GT
[1] "scSS2_25_006"
[1] "scSS2_25_007"
[1] "scSS2_25_008"
[1] "scSS2_25_009"
[1] "scSS2_25_11"
[1] "scSS2_25_12"load first batch
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 14348151 766.3 25334393 1353.1 25334393 1353.1
Vcells 120088880 916.3 351088908 2678.6 438846014 3348.2Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 3648
Number of edges: 121160
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.7558
Number of communities: 12
Elapsed time: 0 seconds
Reclustering of dataset from Desiree
- Exclude sex-related genes – maybe this will already resolve our issues concerning the clustering in terms of biological relevance.
- In case the new clusters are not matching the biological relevance, reclustering based on lists we provide for homeostatic and reactive microglial cells
if you want to save a plot use ggsave(filename = “./output/PNametheplot.pdf”, plotobject))
Define Gene lists
Define Genelist spatial cell types
inspect data
CCA & Harmony integrate Data
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 3228
Number of edges: 91581
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.7795
Number of communities: 12
Elapsed time: 0 seconds
XIST check
Some cells appear to have a low expression of Aif1 as can be seen in the purple shading. However, some of these cells with the low expression seem to be missing later on (see Clustering example). Please check if really only cells with an expression of 0 Aif1 have been excluded
NOTE: We did in the end not fitler for Afip1 negative cells,
inspect unfiltered original RAW data FOR XIST - MIKE TEST
find markers for the Aif1 neg o
Aif1 negative cells were not excluded
Clean integration
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 3228
Number of edges: 91581
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.7326
Number of communities: 12
Elapsed time: 0 seconds
Cell cycle scoring
map cell types
Adipocytes aNSCs Astrocytes
2 19 85
Astrocytes activated B cells Cardiomyocytes
19 1 1
Ependymal Granulocytes Macrophages
2 30 13
Macrophages activated Microglia Microglia activated
2 2911 33
Monocytes Neurons Neurons activated
14 27 40
NK cells NPCs OPCs
1 1 4
qNSCs T cells
2 21 
filter and recluster only Microglia
Re-optimize clustering
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 2944
Number of edges: 108310
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8331
Number of communities: 4
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 2944
Number of edges: 108310
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.7579
Number of communities: 6
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 2944
Number of edges: 108310
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.6942
Number of communities: 6
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 2944
Number of edges: 108310
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.6493
Number of communities: 8
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 2944
Number of edges: 108310
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.6070
Number of communities: 8
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 2944
Number of edges: 108310
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.5735
Number of communities: 9
Elapsed time: 0 seconds
identify optimal rand index
res1 res2 ARI
1 RNA_snn_res.0.2 RNA_snn_res.0.4 0.4149767
2 RNA_snn_res.0.4 RNA_snn_res.0.6 0.6272156
3 RNA_snn_res.0.6 RNA_snn_res.0.8 0.8785492
4 RNA_snn_res.0.8 RNA_snn_res.1 0.9365022
5 RNA_snn_res.1 RNA_snn_res.1.2 0.7298709Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 2944
Number of edges: 108310
Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.6942
Number of communities: 6
Elapsed time: 0 seconds
Map old clusters
Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
Microglia0 28 94 100 103 52 10
Microglia1 1 26 3 4 4 2
Microglia2 128 26 9 3 3 3
Microglia3 0 0 0 0 0 2
Microglia4 4 5 1 4 3 0
Microglia5 12 3 3 0 1 0
Microglia6 Microglia7
Microglia0 17 1
Microglia1 0 0
Microglia2 0 0
Microglia3 0 0
Microglia4 0 12
Microglia5 0 0
Markers for Clusters
--------Summary descriptives table by 'Genotype_Treatment'---------
____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________
WT_Ctrl WT_Stroke APPPS1_Ctrl APPPS1_Stroke p.overall p.WT_Ctrl vs WT_Stroke p.WT_Ctrl vs APPPS1_Ctrl p.WT_Ctrl vs APPPS1_Stroke p.WT_Stroke vs APPPS1_Ctrl p.WT_Stroke vs APPPS1_Stroke p.APPPS1_Ctrl vs APPPS1_Stroke
N=827 N=654 N=825 N=638
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯
labels: <0.001 <0.001 <0.001 . <0.001 <0.001 <0.001
Microglia0 417 (50.4%) 254 (38.8%) 389 (47.2%) 238 (37.3%)
Microglia1 283 (34.2%) 208 (31.8%) 141 (17.1%) 167 (26.2%)
Microglia2 18 (2.18%) 86 (13.1%) 189 (22.9%) 165 (25.9%)
Microglia3 89 (10.8%) 50 (7.65%) 32 (3.88%) 32 (5.02%)
Microglia4 17 (2.06%) 18 (2.75%) 47 (5.70%) 31 (4.86%)
Microglia5 3 (0.36%) 38 (5.81%) 27 (3.27%) 5 (0.78%)
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯
--------Summary descriptives table by 'Genotype_Treatment'---------
__________________________________________________________________________________________________________________________________________________________________________________________________________________________________________
WT_Ctrl WT_Stroke APPPS1_Ctrl APPPS1_Stroke p.overall p.WT_Ctrl vs WT_Stroke p.WT_Ctrl vs APPPS1_Ctrl p.WT_Ctrl vs APPPS1_Stroke p.WT_Stroke vs APPPS1_Ctrl p.WT_Stroke vs APPPS1_Stroke p.APPPS1_Ctrl vs APPPS1_Stroke
N=827 N=654 N=825 N=638
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯
Mouse_ID: 0.000 0.000 0.000 0.000 0.000 0.000 0.000
256#1022 106 (12.8%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
256#1023 93 (11.2%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
364#469 98 (11.9%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
386 0 (0.00%) 33 (5.05%) 0 (0.00%) 0 (0.00%)
387 0 (0.00%) 0 (0.00%) 0 (0.00%) 28 (4.39%)
388 0 (0.00%) 0 (0.00%) 154 (18.7%) 0 (0.00%)
409 0 (0.00%) 95 (14.5%) 0 (0.00%) 0 (0.00%)
41738 0 (0.00%) 0 (0.00%) 0 (0.00%) 160 (25.1%)
41739 0 (0.00%) 0 (0.00%) 0 (0.00%) 178 (27.9%)
41799 0 (0.00%) 181 (27.7%) 0 (0.00%) 0 (0.00%)
42012 0 (0.00%) 163 (24.9%) 0 (0.00%) 0 (0.00%)
42013 0 (0.00%) 0 (0.00%) 0 (0.00%) 181 (28.4%)
42015 165 (20.0%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
42042 0 (0.00%) 182 (27.8%) 0 (0.00%) 0 (0.00%)
42215 181 (21.9%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
42217 184 (22.2%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
42436 0 (0.00%) 0 (0.00%) 179 (21.7%) 0 (0.00%)
42438 0 (0.00%) 0 (0.00%) 171 (20.7%) 0 (0.00%)
42440 0 (0.00%) 0 (0.00%) 171 (20.7%) 0 (0.00%)
457 0 (0.00%) 0 (0.00%) 150 (18.2%) 0 (0.00%)
461 0 (0.00%) 0 (0.00%) 0 (0.00%) 91 (14.3%)
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯
--------Summary descriptives table by 'labels'---------
_____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________
Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5 p.overall p.Microglia0 vs Microglia1 p.Microglia0 vs Microglia2 p.Microglia0 vs Microglia3 p.Microglia0 vs Microglia4 p.Microglia0 vs Microglia5 p.Microglia1 vs Microglia2 p.Microglia1 vs Microglia3 p.Microglia1 vs Microglia4 p.Microglia1 vs Microglia5 p.Microglia2 vs Microglia3 p.Microglia2 vs Microglia4 p.Microglia2 vs Microglia5 p.Microglia3 vs Microglia4 p.Microglia3 vs Microglia5 p.Microglia4 vs Microglia5
N=1298 N=799 N=458 N=203 N=113 N=73
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯
Mouse_ID: . . <0.001 . . . . . . . . . . . . .
256#1022 59 (4.55%) 29 (3.63%) 3 (0.66%) 11 (5.42%) 3 (2.65%) 1 (1.37%)
256#1023 55 (4.24%) 18 (2.25%) 2 (0.44%) 14 (6.90%) 4 (3.54%) 0 (0.00%)
364#469 69 (5.32%) 19 (2.38%) 3 (0.66%) 2 (0.99%) 4 (3.54%) 1 (1.37%)
386 12 (0.92%) 0 (0.00%) 17 (3.71%) 0 (0.00%) 4 (3.54%) 0 (0.00%)
387 11 (0.85%) 1 (0.13%) 10 (2.18%) 5 (2.46%) 1 (0.88%) 0 (0.00%)
388 52 (4.01%) 17 (2.13%) 53 (11.6%) 2 (0.99%) 8 (7.08%) 22 (30.1%)
409 56 (4.31%) 7 (0.88%) 27 (5.90%) 1 (0.49%) 4 (3.54%) 0 (0.00%)
41738 60 (4.62%) 48 (6.01%) 32 (6.99%) 12 (5.91%) 8 (7.08%) 0 (0.00%)
41739 55 (4.24%) 50 (6.26%) 56 (12.2%) 6 (2.96%) 10 (8.85%) 1 (1.37%)
41799 77 (5.93%) 59 (7.38%) 4 (0.87%) 4 (1.97%) 3 (2.65%) 34 (46.6%)
42012 33 (2.54%) 74 (9.26%) 8 (1.75%) 42 (20.7%) 3 (2.65%) 3 (4.11%)
42013 67 (5.16%) 55 (6.88%) 39 (8.52%) 7 (3.45%) 9 (7.96%) 4 (5.48%)
42015 99 (7.63%) 53 (6.63%) 4 (0.87%) 7 (3.45%) 1 (0.88%) 1 (1.37%)
42042 76 (5.86%) 68 (8.51%) 30 (6.55%) 3 (1.48%) 4 (3.54%) 1 (1.37%)
42215 46 (3.54%) 94 (11.8%) 5 (1.09%) 34 (16.7%) 2 (1.77%) 0 (0.00%)
42217 89 (6.86%) 70 (8.76%) 1 (0.22%) 21 (10.3%) 3 (2.65%) 0 (0.00%)
42436 91 (7.01%) 27 (3.38%) 38 (8.30%) 5 (2.46%) 15 (13.3%) 3 (4.11%)
42438 69 (5.32%) 52 (6.51%) 23 (5.02%) 19 (9.36%) 8 (7.08%) 0 (0.00%)
42440 88 (6.78%) 43 (5.38%) 20 (4.37%) 6 (2.96%) 14 (12.4%) 0 (0.00%)
457 89 (6.86%) 2 (0.25%) 55 (12.0%) 0 (0.00%) 2 (1.77%) 2 (2.74%)
461 45 (3.47%) 13 (1.63%) 28 (6.11%) 2 (0.99%) 3 (2.65%) 0 (0.00%)
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ 
all clusters
DAMs
GT_Treat Microglia0 Microglia1 Microglia2 Microglia3 Microglia4
WT_Ctrl 417 283 18 89 17
WT_Stroke 254 208 86 50 18
APPPS1_Ctrl 389 141 189 32 47
APPPS1_Stroke 238 167 165 32 31
DAMs
GT_Treat Microglia5
WT_Ctrl 3
WT_Stroke 38
APPPS1_Ctrl 27
APPPS1_Stroke 5 DAMs
GT_Treat Microglia0 Microglia1 Microglia2 Microglia3 Microglia4
WT_Ctrl 0.504232164 0.342200726 0.021765417 0.107617896 0.020556227
WT_Stroke 0.388379205 0.318042813 0.131498471 0.076452599 0.027522936
APPPS1_Ctrl 0.471515152 0.170909091 0.229090909 0.038787879 0.056969697
APPPS1_Stroke 0.373040752 0.261755486 0.258620690 0.050156740 0.048589342
DAMs
GT_Treat Microglia5
WT_Ctrl 0.003627570
WT_Stroke 0.058103976
APPPS1_Ctrl 0.032727273
APPPS1_Stroke 0.007836991
Pearson's Chi-squared test
data: restab
X-squared = 345.62, df = 15, p-value < 2.2e-16
Dimension Value Microglia0 Microglia1 Microglia2 Microglia3
1 WT_Ctrl Residuals 4.326069 5.399494 -12.519553 5.1749280
2 WT_Ctrl p values 0.000364 0.000002 0.000000 0.0000050
3 WT_Stroke Residuals -3.067114 3.041449 -1.925795 0.8581571
4 WT_Stroke p values 0.051873 0.056506 1.000000 1.0000000
5 APPPS1_Ctrl Residuals 2.087847 -7.650778 6.867393 -4.0307171
6 APPPS1_Ctrl p values 0.883480 0.000000 0.000000 0.0013350
7 APPPS1_Stroke Residuals -3.900527 -0.618951 8.114322 -2.1172634
8 APPPS1_Stroke p values 0.002304 1.000000 0.000000 0.8217000
Microglia4 Microglia5
1 -3.146779 -4.616509
2 0.039619 0.000094
3 -1.639106 6.210771
4 1.000000 0.000000
5 3.275350 1.726722
6 0.025327 1.000000
7 1.516149 -3.112539
8 1.000000 0.044516
old markers
Add Microglia subtype scores
Comparison of DEGs in DAMs between treatments/genotypes
- Subcluster overlaps
We will provide gene lists for different previously described microglia subclusters including homeostatic, DAM 1/DAM2 and IRM identification list. Please generate a Venn diagram or similar to see how big the overlap of ourcells of interest (identified in the scDataset via the spatial transcriptomics list) is with the individual subclusters,
define DAM
Profiles based on genelist provided by Jan Hoffmann
NOT done: Alterantive DAM profiles based on Cell. 2017 Jun 15;169(7):1276-1290.e17. doi: 10.1016/j.cell.2017.05.018)
DAM1
Clusters
DAMs Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
FALSE 0.969183359 0.992490613 0.460698690 0.995073892 0.876106195 0.739726027
TRUE 0.030816641 0.007509387 0.539301310 0.004926108 0.123893805 0.260273973
Clusters
DAM2 Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
FALSE 0.973035439 0.992490613 0.502183406 0.995073892 0.911504425 0.767123288
TRUE 0.026964561 0.007509387 0.497816594 0.004926108 0.088495575 0.232876712 DAMs
DAM2 FALSE TRUE
FALSE 0.98318686 0.22629969
TRUE 0.01681314 0.77370031
proportion tables show percentages of DAM cells per condition
DAMs
GT_Treat FALSE TRUE
WT_Ctrl 827 0
WT_Stroke 608 46
APPPS1_Ctrl 653 172
APPPS1_Stroke 529 109 DAMs
GT_Treat FALSE TRUE
WT_Ctrl 1.00000000 0.00000000
WT_Stroke 0.92966361 0.07033639
APPPS1_Ctrl 0.79151515 0.20848485
APPPS1_Stroke 0.82915361 0.17084639
Pearson's Chi-squared test
data: restab
X-squared = 216.7, df = 3, p-value < 2.2e-16
Dimension Value FALSE TRUE
1 WT_Ctrl Residuals 11.987628 -11.987628
2 WT_Ctrl p values 0.000000 0.000000
3 WT_Stroke Residuals 3.759161 -3.759161
4 WT_Stroke p values 0.001364 0.001364
5 APPPS1_Ctrl Residuals -10.495487 10.495487
6 APPPS1_Ctrl p values 0.000000 0.000000
7 APPPS1_Stroke Residuals -5.428963 5.428963
8 APPPS1_Stroke p values 0.000000 0.000000a) DAMs in APPPS1 vs. DAMs in APPPS1 + Stroke – Venn diagram, or similar
DAMs
GT_Treat FALSE TRUE
APPPS1_Ctrl 653 172
APPPS1_Stroke 529 109 DAMs
GT_Treat FALSE TRUE
APPPS1_Ctrl 0.7915152 0.2084848
APPPS1_Stroke 0.8291536 0.1708464
Fisher's Exact Test for Count Data
data: restab
p-value = 0.07119
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
0.593415 1.028605
sample estimates:
odds ratio
0.7824 
b) DAMs in WT+Stroke vs. DAMs in APPPS1 + Stroke – Venn diagram, or similar
DAMs
GT_Treat FALSE TRUE
WT_Ctrl 827 0
WT_Stroke 608 46 DAMs
GT_Treat FALSE TRUE
WT_Ctrl 1.00000000 0.00000000
WT_Stroke 0.92966361 0.07033639
Fisher's Exact Test for Count Data
data: restab
p-value < 2.2e-16
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
16.1857 Inf
sample estimates:
odds ratio
Inf 
c) Separation of DAMs into DAM1 and DAM2 (with a provided gene list), repetition of a) and b) to see if our cells on interest overlap more with one or the other profile
DAM2
GT_Treat FALSE TRUE
WT_Ctrl 0 0
WT_Stroke 27 19
APPPS1_Ctrl 13 159
APPPS1_Stroke 34 75 DAM2
GT_Treat FALSE TRUE
WT_Ctrl
WT_Stroke 0.5869565 0.4130435
APPPS1_Ctrl 0.0755814 0.9244186
APPPS1_Stroke 0.3119266 0.6880734
Pearson's Chi-squared test
data: restab
X-squared = NaN, df = 3, p-value = NA Dimension Value FALSE TRUE
1 WT_Ctrl Residuals NaN NaN
2 WT_Ctrl p values NaN NaN
3 WT_Stroke Residuals 6.306166 -6.306166
4 WT_Stroke p values 0.000000 0.000000
5 APPPS1_Ctrl Residuals -6.861355 6.861355
6 APPPS1_Ctrl p values 0.000000 0.000000
7 APPPS1_Stroke Residuals 2.616621 -2.616621
8 APPPS1_Stroke p values 0.071044 0.071044
DAM2
GT_Treat FALSE TRUE
APPPS1_Ctrl 13 159
APPPS1_Stroke 34 75 DAM2
GT_Treat FALSE TRUE
APPPS1_Ctrl 0.0755814 0.9244186
APPPS1_Stroke 0.3119266 0.6880734
Pearson's Chi-squared test with Yates' continuity correction
data: restab
X-squared = 25.087, df = 1, p-value = 5.479e-07
DAM2
GT_Treat FALSE TRUE
WT_Stroke 27 19 DAM2
GT_Treat FALSE TRUE
WT_Stroke 0.5869565 0.4130435
Chi-squared test for given probabilities
data: restab
X-squared = 1.3913, df = 1, p-value = 0.2382
Homeostatic Cells
Clusters
Homeo Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
FALSE 0.2681048 0.3504380 0.8515284 0.7241379 0.4513274 0.3835616
TRUE 0.7318952 0.6495620 0.1484716 0.2758621 0.5486726 0.6164384
Homeo vs DAM
Homeo
GT_Treat Neither Homeo DAM Unknown
WT_Ctrl 213 614 0 0
WT_Stroke 239 369 44 2
APPPS1_Ctrl 203 450 164 8
APPPS1_Stroke 277 252 104 5 Homeo
GT_Treat Neither Homeo DAM Unknown
WT_Ctrl 0.257557437 0.742442563 0.000000000 0.000000000
WT_Stroke 0.365443425 0.564220183 0.067278287 0.003058104
APPPS1_Ctrl 0.246060606 0.545454545 0.198787879 0.009696970
APPPS1_Stroke 0.434169279 0.394984326 0.163009404 0.007836991
Pearson's Chi-squared test
data: restab
X-squared = 325.49, df = 9, p-value < 2.2e-16 Dimension Value Neither Homeo DAM Unknown
1 WT_Ctrl Residuals -4.302951 11.6592377 -11.676040 -2.426874
2 WT_Ctrl p values 0.000270 0.0000000 0.000000 0.243673
3 WT_Stroke Residuals 3.046313 -0.4765131 -3.645594 -0.829592
4 WT_Stroke p values 0.037067 1.0000000 0.004268 1.000000
5 APPPS1_Ctrl Residuals -5.132521 -1.8405306 10.208007 2.188247
6 APPPS1_Ctrl p values 0.000005 1.0000000 0.000000 0.458426
7 APPPS1_Stroke Residuals 7.215188 -10.2316455 5.287851 1.099084
8 APPPS1_Stroke p values 0.000000 0.0000000 0.000002 1.000000
Homeo
Clust Neither Homeo DAM Unknown
Microglia0 310 948 38 2
Microglia1 276 517 4 2
Microglia2 150 61 240 7
Microglia3 147 55 0 1
Microglia4 38 61 13 1
Microglia5 11 43 17 2 Homeo
Clust Neither Homeo DAM Unknown
Microglia0 0.238828968 0.730354391 0.029275809 0.001540832
Microglia1 0.345431790 0.647058824 0.005006258 0.002503129
Microglia2 0.327510917 0.133187773 0.524017467 0.015283843
Microglia3 0.724137931 0.270935961 0.000000000 0.004926108
Microglia4 0.336283186 0.539823009 0.115044248 0.008849558
Microglia5 0.150684932 0.589041096 0.232876712 0.027397260
Pearson's Chi-squared test
data: restab
X-squared = 1349.2, df = 15, p-value < 2.2e-16 Dimension Value Neither Homeo DAM Unknown
1 Microglia0 Residuals -8.0536268 15.3880640 -12.0065476 -2.40533213
2 Microglia0 p values 0.0000000 0.0000000 0.0000000 0.38778700
3 Microglia1 Residuals 2.0543582 5.0006029 -10.8629350 -1.20557087
4 Microglia1 p values 0.9585850 0.0000140 0.0000000 1.00000000
5 Microglia2 Residuals 0.5474935 -20.6729086 31.6290145 3.33275814
6 Microglia2 p values 1.0000000 0.0000000 0.0000000 0.02063800
7 Microglia3 Residuals 12.9381381 -8.9960457 -5.0838972 -0.03504955
8 Microglia3 p values 0.0000000 0.0000000 0.0000090 1.00000000
9 Microglia4 Residuals 0.4592792 -0.7127124 0.3192794 0.57163244
10 Microglia4 p values 1.0000000 1.0000000 1.0000000 1.00000000
11 Microglia5 Residuals -3.0856938 0.2918834 3.5668728 2.71014789
12 Microglia5 p values 0.0487390 1.0000000 0.0086700 0.16140800
Celltype
Clust 256#1022 256#1023 364#469 386 387 388 409 41738 41739 41799 42012
Microglia0 59 55 69 12 11 52 56 60 55 77 33
Microglia1 29 18 19 0 1 17 7 48 50 59 74
Microglia2 3 2 3 17 10 53 27 32 56 4 8
Microglia3 11 14 2 0 5 2 1 12 6 4 42
Microglia4 3 4 4 4 1 8 4 8 10 3 3
Microglia5 1 0 1 0 0 22 0 0 1 34 3
Celltype
Clust 42013 42015 42042 42215 42217 42436 42438 42440 457 461
Microglia0 67 99 76 46 89 91 69 88 89 45
Microglia1 55 53 68 94 70 27 52 43 2 13
Microglia2 39 4 30 5 1 38 23 20 55 28
Microglia3 7 7 3 34 21 5 19 6 0 2
Microglia4 9 1 4 2 3 15 8 14 2 3
Microglia5 4 1 1 0 0 3 0 0 2 0 Celltype
Clust 256#1022 256#1023 364#469 386 387
Microglia0 0.045454545 0.042372881 0.053158706 0.009244992 0.008474576
Microglia1 0.036295369 0.022528160 0.023779725 0.000000000 0.001251564
Microglia2 0.006550218 0.004366812 0.006550218 0.037117904 0.021834061
Microglia3 0.054187192 0.068965517 0.009852217 0.000000000 0.024630542
Microglia4 0.026548673 0.035398230 0.035398230 0.035398230 0.008849558
Microglia5 0.013698630 0.000000000 0.013698630 0.000000000 0.000000000
Celltype
Clust 388 409 41738 41739 41799
Microglia0 0.040061633 0.043143297 0.046224961 0.042372881 0.059322034
Microglia1 0.021276596 0.008760951 0.060075094 0.062578223 0.073842303
Microglia2 0.115720524 0.058951965 0.069868996 0.122270742 0.008733624
Microglia3 0.009852217 0.004926108 0.059113300 0.029556650 0.019704433
Microglia4 0.070796460 0.035398230 0.070796460 0.088495575 0.026548673
Microglia5 0.301369863 0.000000000 0.000000000 0.013698630 0.465753425
Celltype
Clust 42012 42013 42015 42042 42215
Microglia0 0.025423729 0.051617874 0.076271186 0.058551618 0.035439137
Microglia1 0.092615770 0.068836045 0.066332916 0.085106383 0.117647059
Microglia2 0.017467249 0.085152838 0.008733624 0.065502183 0.010917031
Microglia3 0.206896552 0.034482759 0.034482759 0.014778325 0.167487685
Microglia4 0.026548673 0.079646018 0.008849558 0.035398230 0.017699115
Microglia5 0.041095890 0.054794521 0.013698630 0.013698630 0.000000000
Celltype
Clust 42217 42436 42438 42440 457
Microglia0 0.068567026 0.070107858 0.053158706 0.067796610 0.068567026
Microglia1 0.087609512 0.033792240 0.065081352 0.053817272 0.002503129
Microglia2 0.002183406 0.082969432 0.050218341 0.043668122 0.120087336
Microglia3 0.103448276 0.024630542 0.093596059 0.029556650 0.000000000
Microglia4 0.026548673 0.132743363 0.070796460 0.123893805 0.017699115
Microglia5 0.000000000 0.041095890 0.000000000 0.000000000 0.027397260
Celltype
Clust 461
Microglia0 0.034668721
Microglia1 0.016270338
Microglia2 0.061135371
Microglia3 0.009852217
Microglia4 0.026548673
Microglia5 0.000000000
Pearson's Chi-squared test
data: restab
X-squared = 1161.7, df = 100, p-value < 2.2e-16 Dimension Value 256#1022 256#1023 364#469 386
1 Microglia0 Residuals 2.44377348 2.9705510 5.3371695 -0.8989740
2 Microglia0 p values 1.00000000 0.3745550 0.0000120 1.0000000
3 Microglia1 Residuals 0.05153557 -1.7156438 -1.7552529 -3.5258555
4 Microglia1 p values 1.00000000 1.0000000 1.0000000 0.0531870
5 Microglia2 Residuals -3.68206945 -3.6247877 -3.4712387 5.7313357
6 Microglia2 p values 0.02915000 0.0364390 0.0652760 0.0000010
7 Microglia3 Residuals 1.44104299 3.1553761 -1.9290790 -1.5721655
8 Microglia3 p values 1.00000000 0.2019670 1.0000000 1.0000000
9 Microglia4 Residuals -0.55024909 0.2360458 0.1275165 2.4906670
10 Microglia4 p values 1.00000000 1.0000000 1.0000000 1.0000000
11 Microglia5 Residuals -1.03592849 -1.5626316 -0.9448057 -0.9211908
12 Microglia5 p values 1.00000000 1.0000000 1.0000000 1.0000000
387 388 409 41738 41739 41799
1 -0.51444512 -2.6505570 2.9649778 -1.7264092 -3.6568691 -0.4330528
2 1.00000000 1.0000000 0.3814080 1.0000000 0.0321700 1.0000000
3 -2.81797531 -4.6156234 -4.4052992 0.8366028 0.2940361 1.7041261
4 0.60892700 0.0004940 0.0013310 1.0000000 1.0000000 1.0000000
5 2.95691820 6.6326832 3.5165321 1.5944787 6.0395281 -5.1139895
6 0.39152000 0.0000000 0.0550900 1.0000000 0.0000000 0.0000400
7 2.30022232 -2.8157419 -2.2847410 0.3103929 -1.9146843 -2.5680472
8 1.00000000 0.6131760 1.0000000 1.0000000 1.0000000 1.0000000
9 -0.07386006 0.9000619 0.1919563 0.7865226 1.2750261 -1.5764257
10 1.00000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
11 -0.84781089 9.6781691 -1.5798990 -2.0741450 -1.6975433 14.5611594
12 1.00000000 0.0000000 1.0000000 1.0000000 1.0000000 0.0000000
42012 42013 42015 42042 42215 42217 42436
1 -6.3085838 -1.9783952 4.236734 -0.6540351 -5.223614 1.207651 1.876414
2 0.0000000 1.0000000 0.002858 1.0000000 0.000022 1.000000 1.000000
3 5.3936885 1.0139659 1.481007 3.2019076 7.743028 3.435115 -3.742891
4 0.0000090 1.0000000 1.000000 0.1720160 0.000000 0.074630 0.022921
5 -3.8594836 2.2950468 -4.790482 0.3560163 -4.902303 -5.803129 2.160416
6 0.0143170 1.0000000 0.000210 1.0000000 0.000119 0.000001 1.000000
7 9.7837126 -1.6596083 -1.384306 -2.8843069 6.516341 2.497885 -2.235052
8 0.0000000 1.0000000 1.000000 0.4942680 0.000000 1.000000 1.000000
9 -1.3659921 0.8197522 -2.224338 -1.1893265 -1.975789 -1.610006 3.263494
10 1.0000000 1.0000000 1.000000 1.0000000 1.000000 1.000000 0.138660
11 -0.5398963 -0.2408341 -1.592919 -1.7288124 -2.214433 -2.233923 -0.713461
12 1.0000000 1.0000000 1.000000 1.0000000 1.000000 1.000000 1.000000
42438 42440 457 461
1 -1.0146340 2.0006974 3.8599005 1.0463090
2 1.0000000 1.0000000 0.0142930 1.0000000
3 0.9906319 -0.6041055 -7.2959710 -2.8011450
4 1.0000000 1.0000000 0.0000000 0.6416130
5 -0.7831848 -1.4353711 7.3221036 4.0670945
6 1.0000000 1.0000000 0.0000000 0.0059980
7 2.2418170 -1.8009111 -3.4213290 -1.7965860
8 1.0000000 1.0000000 0.0785180 1.0000000
9 0.5891480 3.0499452 -1.6392099 -0.2731842
10 1.0000000 0.2883930 1.0000000 1.0000000
11 -2.1485074 -2.1485074 -0.9267321 -1.5451959
12 1.0000000 1.0000000 1.0000000 1.0000000
Clust
gender Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
f 444 251 124 27 35 7
m 854 548 334 176 78 66 Clust
gender Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
f 0.500000000 0.282657658 0.139639640 0.030405405 0.039414414 0.007882883
m 0.415369650 0.266536965 0.162451362 0.085603113 0.037937743 0.032101167
Pearson's Chi-squared test
data: restab
X-squared = 54.849, df = 5, p-value = 1.402e-10 Dimension Value Microglia0 Microglia1 Microglia2 Microglia3 Microglia4
1 f Residuals 4.244835 0.9027835 -1.567335 -5.425071 0.1914087
2 f p values 0.000263 1.0000000 1.000000 0.000001 1.0000000
3 m Residuals -4.244835 -0.9027835 1.567335 5.425071 -0.1914087
4 m p values 0.000263 1.0000000 1.000000 0.000001 1.0000000
Microglia5
1 -3.878397
2 0.001262
3 3.878397
4 0.001262
d) Homeostatic microglia (with provided gene list) in APPPS1 vs. Homeostatic microglia in APPPS1 + Stroke – Venn diagram, or similar
proportion tables show percentages of Homeostatic cells per condition
Homeo
GT_Treat FALSE TRUE
WT_Ctrl 213 614
WT_Stroke 283 371
APPPS1_Ctrl 367 458
APPPS1_Stroke 381 257 Homeo
GT_Treat FALSE TRUE
WT_Ctrl 0.2575574 0.7424426
WT_Stroke 0.4327217 0.5672783
APPPS1_Ctrl 0.4448485 0.5551515
APPPS1_Stroke 0.5971787 0.4028213
Pearson's Chi-squared test
data: restab
X-squared = 173.96, df = 3, p-value < 2.2e-16 Dimension Value FALSE TRUE
1 WT_Ctrl Residuals -11.3276598 11.3276598
2 WT_Ctrl p values 0.0000000 0.0000000
3 WT_Stroke Residuals 0.5968313 -0.5968313
4 WT_Stroke p values 1.0000000 1.0000000
5 APPPS1_Ctrl Residuals 1.5280030 -1.5280030
6 APPPS1_Ctrl p values 1.0000000 1.0000000
7 APPPS1_Stroke Residuals 10.0892181 -10.0892181
8 APPPS1_Stroke p values 0.0000000 0.0000000
e) Homeostatic microglia in WT+Stroke vs. Homeostatic microglia in APPPS1 + Stroke – Venn diagram, or similar
Homeo
GT_Treat FALSE TRUE
APPPS1_Ctrl 367 458
APPPS1_Stroke 381 257 Homeo
GT_Treat FALSE TRUE
APPPS1_Ctrl 0.4448485 0.5551515
APPPS1_Stroke 0.5971787 0.4028213
Pearson's Chi-squared test with Yates' continuity correction
data: restab
X-squared = 32.804, df = 1, p-value = 1.02e-08
Homeo
GT_Treat FALSE TRUE
WT_Ctrl 213 614
WT_Stroke 283 371 Homeo
GT_Treat FALSE TRUE
WT_Ctrl 0.2575574 0.7424426
WT_Stroke 0.4327217 0.5672783
Pearson's Chi-squared test with Yates' continuity correction
data: restab
X-squared = 49.522, df = 1, p-value = 1.962e-12
DISTAL
Clusters
Distals Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
FALSE 0.7688752 0.6958698 0.3864629 0.8029557 0.6548673 0.6301370
TRUE 0.2311248 0.3041302 0.6135371 0.1970443 0.3451327 0.3698630
Clusters
Controls Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
FALSE 0.4522342 0.4856070 0.5567686 0.5714286 0.5309735 0.5342466
TRUE 0.5477658 0.5143930 0.4432314 0.4285714 0.4690265 0.4657534
Clusters
Strokes Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
FALSE 0.7349769 0.7909887 0.1462882 0.9408867 0.3982301 0.4383562
TRUE 0.2650231 0.2090113 0.8537118 0.0591133 0.6017699 0.5616438
proportion tables show percebtages of DAM cells per condition
Distals binary proportions
Distals
GT_Treat FALSE TRUE
WT_Ctrl 641 186
WT_Stroke 496 158
APPPS1_Ctrl 494 331
APPPS1_Stroke 383 255 Distals
GT_Treat FALSE TRUE
WT_Ctrl 0.7750907 0.2249093
WT_Stroke 0.7584098 0.2415902
APPPS1_Ctrl 0.5987879 0.4012121
APPPS1_Stroke 0.6003135 0.3996865
Pearson's Chi-squared test
data: restab
X-squared = 96.905, df = 3, p-value < 2.2e-16
Dimension Value FALSE TRUE
1 WT_Ctrl Residuals 6.637572 -6.637572
2 WT_Ctrl p values 0.000000 0.000000
3 WT_Stroke Residuals 4.634828 -4.634828
4 WT_Stroke p values 0.000029 0.000029
5 APPPS1_Ctrl Residuals -6.213329 6.213329
6 APPPS1_Ctrl p values 0.000000 0.000000
7 APPPS1_Stroke Residuals -5.144074 5.144074
8 APPPS1_Stroke p values 0.000002 0.000002a) Distals in APPPS1 vs. DAMs in APPPS1 + Stroke – Venn diagram, or similar
Distals
GT_Treat FALSE TRUE
APPPS1_Ctrl 494 331
APPPS1_Stroke 383 255 Distals
GT_Treat FALSE TRUE
APPPS1_Ctrl 0.5987879 0.4012121
APPPS1_Stroke 0.6003135 0.3996865
Fisher's Exact Test for Count Data
data: restab
p-value = 0.9572
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
0.8000638 1.2337160
sample estimates:
odds ratio
0.9936697 
b) Distals in WT+Stroke vs. DAMs in APPPS1 + Stroke – Venn diagram, or similar
Distals
GT_Treat FALSE TRUE
WT_Ctrl 641 186
WT_Stroke 496 158 Distals
GT_Treat FALSE TRUE
WT_Ctrl 0.7750907 0.2249093
WT_Stroke 0.7584098 0.2415902
Fisher's Exact Test for Count Data
data: restab
p-value = 0.4577
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
0.8547616 1.4087562
sample estimates:
odds ratio
1.097723 
Controls binary proportions
Controls
GT_Treat FALSE TRUE
WT_Ctrl 324 503
WT_Stroke 321 333
APPPS1_Ctrl 455 370
APPPS1_Stroke 345 293 Controls
GT_Treat FALSE TRUE
WT_Ctrl 0.3917775 0.6082225
WT_Stroke 0.4908257 0.5091743
APPPS1_Ctrl 0.5515152 0.4484848
APPPS1_Stroke 0.5407524 0.4592476
Pearson's Chi-squared test
data: restab
X-squared = 50.986, df = 3, p-value = 4.925e-11
Dimension Value FALSE TRUE
1 WT_Ctrl Residuals -6.7193065248 6.7193065248
2 WT_Ctrl p values 0.0000000000 0.0000000000
3 WT_Stroke Residuals -0.0001807502 0.0001807502
4 WT_Stroke p values 1.0000000000 1.0000000000
5 APPPS1_Ctrl Residuals 4.1098357128 -4.1098357128
6 APPPS1_Ctrl p values 0.0003170000 0.0003170000
7 APPPS1_Stroke Residuals 2.8500868085 -2.8500868085
8 APPPS1_Stroke p values 0.0349660000 0.0349660000a) Controls in APPPS1 vs. DAMs in APPPS1 + Stroke – Venn diagram, or similar
Controls
GT_Treat FALSE TRUE
APPPS1_Ctrl 455 370
APPPS1_Stroke 345 293 Controls
GT_Treat FALSE TRUE
APPPS1_Ctrl 0.5515152 0.4484848
APPPS1_Stroke 0.5407524 0.4592476
Fisher's Exact Test for Count Data
data: restab
p-value = 0.7109
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
0.8439753 1.2922035
sample estimates:
odds ratio
1.044378 
b) Controls in WT+Stroke vs. DAMs in APPPS1 + Stroke – Venn diagram, or similar
Controls
GT_Treat FALSE TRUE
WT_Ctrl 324 503
WT_Stroke 321 333 Controls
GT_Treat FALSE TRUE
WT_Ctrl 0.3917775 0.6082225
WT_Stroke 0.4908257 0.5091743
Fisher's Exact Test for Count Data
data: restab
p-value = 0.0001448
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
0.5401406 0.8267237
sample estimates:
odds ratio
0.6684173 
Strokes binary proportions
Peri_Ictal
GT_Treat FALSE TRUE
WT_Ctrl 806 21
WT_Stroke 395 259
APPPS1_Ctrl 441 384
APPPS1_Stroke 279 359 Peri_Ictal
GT_Treat FALSE TRUE
WT_Ctrl 0.97460701 0.02539299
WT_Stroke 0.60397554 0.39602446
APPPS1_Ctrl 0.53454545 0.46545455
APPPS1_Stroke 0.43730408 0.56269592
Pearson's Chi-squared test
data: restab
X-squared = 566.14, df = 3, p-value < 2.2e-16
Dimension Value FALSE TRUE
1 WT_Ctrl Residuals 22.939260 -22.939260
2 WT_Ctrl p values 0.000000 0.000000
3 WT_Stroke Residuals -2.955689 2.955689
4 WT_Stroke p values 0.024958 0.024958
5 APPPS1_Ctrl Residuals -8.387478 8.387478
6 APPPS1_Ctrl p values 0.000000 0.000000
7 APPPS1_Stroke Residuals -12.898742 12.898742
8 APPPS1_Stroke p values 0.000000 0.000000a) Strokes in APPPS1 vs. DAMs in APPPS1 + Stroke – Venn diagram, or similar
Peri_Ictal
GT_Treat FALSE TRUE
APPPS1_Ctrl 441 384
APPPS1_Stroke 279 359 Peri_Ictal
GT_Treat FALSE TRUE
APPPS1_Ctrl 0.5345455 0.4654545
APPPS1_Stroke 0.4373041 0.5626959
Fisher's Exact Test for Count Data
data: restab
p-value = 0.0002717
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
1.193924 1.829163
sample estimates:
odds ratio
1.477309 
b) Strokes in WT+Stroke vs. DAMs in APPPS1 + Stroke – Venn diagram, or similar
Peri_Ictal
GT_Treat FALSE TRUE
WT_Ctrl 806 21
WT_Stroke 395 259 Peri_Ictal
GT_Treat FALSE TRUE
WT_Ctrl 0.97460701 0.02539299
WT_Stroke 0.60397554 0.39602446
Fisher's Exact Test for Count Data
data: restab
p-value < 2.2e-16
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
15.78008 41.91214
sample estimates:
odds ratio
25.11696 
Alternative appraoch to identify cell types (assuming the cell types are mutaully exclusive)
DEG comparing conditions overall
WT Stroke vs no Stroke
avg_logFC: log fold-chage of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first group
character(0)
APPPS1 Stroke vs APPPS1 no Stroke
avg_logFC: log fold-chage of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first group
[1] "AC121793.2" "Olfr907" "S100a6" 
WT Stroke vs APPPS1Stroke
[1] "Lilrb4"
WT ctr; vs APPPS1 ctrl
avg_logFC: log fold-chage of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first group
[1] "Olfr633" "Olfr1178"
Scatterplot of DEGs of all four conditions, see https://www.nature.com/articles/s41593-023-01355-y ; see Fig 1e
[1] "S100a6 cannot be found"
[1] "S100a6 cannot be found" "Atp1a2 cannot be found" "Fn1 cannot be found"
[4] "Ntrk2 cannot be found" 
DAMS in APPS1 Wt vs Stroke
to do selection of DAMS only compare APPPS1CTRL vs APPS1 Stroke to do selection of DAMs only compare APPPS1Stroke vs WT_Stroke
Dot plot showing top markers for condition clusters, same paper Fig 2f
TEST - Mike
### TEST - Mike
DEG comparing Cluster
All Clusters versus All Clusters
Define Main analysis pipeline
DEG run for each combination
[1] "Microglia0_vs_Microglia1"
[1] "all"[1] "comorbid"[1] "Microglia0_vs_Microglia2"
[1] "all"[1] "comorbid"[1] "Microglia0_vs_Microglia3"
[1] "all"[1] "comorbid"[1] "Microglia0_vs_Microglia4"
[1] "all"[1] "comorbid"[1] "Microglia0_vs_Microglia5"
[1] "all"[1] "comorbid"[1] "Microglia1_vs_Microglia2"
[1] "all"[1] "comorbid"[1] "Microglia1_vs_Microglia3"
[1] "all"[1] "comorbid"[1] "Microglia1_vs_Microglia4"
[1] "all"[1] "comorbid"[1] "Microglia1_vs_Microglia5"
[1] "all"[1] "comorbid"[1] "Microglia2_vs_Microglia3"
[1] "all"[1] "comorbid"[1] "Microglia2_vs_Microglia4"
[1] "all"[1] "comorbid"[1] "Microglia2_vs_Microglia5"
[1] "all"[1] "comorbid"[1] "Microglia3_vs_Microglia4"
[1] "all"[1] "comorbid"[1] "Microglia3_vs_Microglia5"
[1] "all"[1] "comorbid"[1] "Microglia4_vs_Microglia5"
[1] "all"[1] "comorbid"Microglia0_vs_Microglia1
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-2.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Trac | 0 | -1.7063491 | 0.660 | 0.869 | 0 |
| Arfgef3 | 0 | -1.0887626 | 0.665 | 0.874 | 0 |
| Vmn1r218 | 0 | 0.8801728 | 0.898 | 0.717 | 0 |
| Cpa6 | 0 | 1.3559398 | 0.760 | 0.522 | 0 |
| Lipe | 0 | -1.1115953 | 0.851 | 0.935 | 0 |
| Or4f14b | 0 | 0.9868262 | 0.956 | 0.832 | 0 |
| Or51q1 | 0 | 0.8486383 | 0.922 | 0.778 | 0 |
| Vmn1r201 | 0 | 1.8546872 | 0.588 | 0.344 | 0 |
| Fgd4 | 0 | 0.4592167 | 0.933 | 0.805 | 0 |
| Vmn1r76 | 0 | 1.3102043 | 0.810 | 0.615 | 0 |
| Or13a17 | 0 | 0.5632069 | 0.797 | 0.593 | 0 |
| Vmn1r81 | 0 | 1.0998458 | 0.935 | 0.791 | 0 |
| Or1f19 | 0 | 1.1797206 | 0.800 | 0.603 | 0 |
| Vmn1r6 | 0 | 1.0752258 | 0.739 | 0.533 | 0 |
| Or6z3 | 0 | 0.8587296 | 0.901 | 0.741 | 0 |
| Psg16 | 0 | 0.8487776 | 0.820 | 0.605 | 0 |
| Cyb5r4 | 0 | 0.8345815 | 0.733 | 0.529 | 0 |
| Nipal2 | 0 | 0.7547669 | 0.817 | 0.630 | 0 |
| Or13a18 | 0 | 0.7794006 | 0.844 | 0.701 | 0 |
| Slc38a6 | 0 | 0.6364006 | 0.893 | 0.718 | 0 |
| Sik2 | 0 | 0.5163416 | 0.878 | 0.708 | 0 |
| Or13a25 | 0 | 0.8214713 | 0.767 | 0.552 | 0 |
| Traf5 | 0 | 0.3551980 | 0.794 | 0.608 | 0 |
| Snhg14 | 0 | 1.0264191 | 0.911 | 0.762 | 0 |
| Or6c6c | 0 | 0.6616574 | 0.723 | 0.507 | 0 |
| Zfp369 | 0 | 0.4648512 | 0.871 | 0.666 | 0 |
| Sros1 | 0 | 0.8076862 | 0.812 | 0.646 | 0 |
| Vmn1r197 | 0 | 1.2872492 | 0.785 | 0.611 | 0 |
| Cep112it | 0 | 1.0929949 | 0.611 | 0.395 | 0 |
| Or6c8 | 0 | 1.5051352 | 0.669 | 0.462 | 0 |
| Cux2 | 0 | -0.9025422 | 0.808 | 0.924 | 0 |
| Prdm11 | 0 | 0.4472788 | 0.614 | 0.385 | 0 |
| Acad9 | 0 | 0.4533341 | 0.787 | 0.612 | 0 |
| Hsd3b2 | 0 | 1.9297267 | 0.635 | 0.442 | 0 |
| Cul4a | 0 | 0.7300919 | 0.729 | 0.547 | 0 |
| Slfn3 | 0 | 0.5367422 | 0.700 | 0.483 | 0 |
| Eif2a | 0 | -0.7878757 | 0.865 | 0.937 | 0 |
| Or10ag54 | 0 | 0.8337652 | 0.820 | 0.650 | 0 |
| Vmn1r46 | 0 | 0.8794171 | 0.794 | 0.602 | 0 |
| Or10h28 | 0 | 0.7131371 | 0.790 | 0.615 | 0 |
| Nopchap1 | 0 | 0.8011462 | 0.986 | 0.934 | 0 |
| Vmn1r18 | 0 | 1.1206616 | 0.776 | 0.596 | 0 |
| Or52k2 | 0 | 0.8714795 | 0.703 | 0.523 | 0 |
| Or1ab2 | 0 | 0.9178200 | 0.773 | 0.586 | 0 |
| Maip1 | 0 | 0.5767887 | 0.650 | 0.447 | 0 |
| Or4a77 | 0 | 1.4103791 | 0.671 | 0.458 | 0 |
| Or1j15 | 0 | 0.9185293 | 0.849 | 0.723 | 0 |
| Or51k1 | 0 | 1.1480351 | 0.812 | 0.667 | 0 |
| Vmn1r58 | 0 | 0.8989285 | 0.767 | 0.576 | 0 |
| Pax6 | 0 | -0.9621078 | 0.720 | 0.846 | 0 |
| Tmcc1 | 0 | 0.3037596 | 0.914 | 0.797 | 0 |
| Or4c115 | 0 | 1.3483142 | 0.591 | 0.390 | 0 |
| Bltp1 | 0 | 0.5276250 | 0.713 | 0.506 | 0 |
| Grip2 | 0 | 1.4998994 | 0.881 | 0.777 | 0 |
| Senp7 | 0 | 0.3728211 | 0.830 | 0.671 | 0 |
| Grk4 | 0 | 0.6580214 | 0.807 | 0.642 | 0 |
| Lars2 | 0 | -0.2339387 | 0.833 | 0.682 | 0 |
| Ucp2 | 0 | 0.7092400 | 0.421 | 0.210 | 0 |
| Kcnq1ot1 | 0 | 0.4429731 | 0.971 | 0.907 | 0 |
| Or6c208 | 0 | 1.0712086 | 0.675 | 0.479 | 0 |
| Or52m1 | 0 | -1.4214082 | 0.659 | 0.807 | 0 |
| 9930111J21Rik2 | 0 | 0.2874189 | 0.918 | 0.768 | 0 |
| Or7g23 | 0 | 0.7463336 | 0.740 | 0.591 | 0 |
| Ranbp3l | 0 | 0.8859967 | 0.735 | 0.532 | 0 |
| Cep290 | 0 | -0.9642513 | 0.828 | 0.916 | 0 |
| Ccdc82 | 0 | 0.7570261 | 0.717 | 0.542 | 0 |
| St14 | 0 | 0.6868633 | 0.671 | 0.471 | 0 |
| Nox4 | 0 | 0.4297913 | 0.600 | 0.370 | 0 |
| Ift20 | 0 | -0.7147168 | 0.729 | 0.872 | 0 |
| Zfp65 | 0 | 0.5765027 | 0.545 | 0.349 | 0 |
| Lpl | 0 | 0.3464301 | 0.739 | 0.541 | 0 |
| Rrm1 | 0 | 0.2793334 | 0.721 | 0.543 | 0 |
| Or5b124 | 0 | 0.9798651 | 0.686 | 0.534 | 0 |
| Nom1 | 0 | 0.7170819 | 0.793 | 0.617 | 0 |
| Bora | 0 | 0.5744559 | 0.504 | 0.307 | 0 |
| Pign | 0 | 0.4839414 | 0.810 | 0.631 | 0 |
| Vmn1r72 | 0 | 0.7085967 | 0.716 | 0.537 | 0 |
| Dpf1 | 0 | -0.7708053 | 0.531 | 0.682 | 0 |
| Macrod2os1 | 0 | 0.8181883 | 0.522 | 0.327 | 0 |
| Pi15 | 0 | 0.9551680 | 0.636 | 0.442 | 0 |
| Cflar | 0 | 0.1832956 | 0.827 | 0.677 | 0 |
| Glrx2 | 0 | 0.3575157 | 0.751 | 0.572 | 0 |
| Ncf2 | 0 | 0.3230060 | 0.720 | 0.523 | 0 |
| Zfp738 | 0 | 0.4564973 | 0.831 | 0.667 | 0 |
| Cnpy3 | 0 | 0.6840410 | 0.550 | 0.347 | 0 |
| Or4p4 | 0 | 0.9283994 | 0.733 | 0.548 | 0 |
| mt-Tq | 0 | -1.4433784 | 0.689 | 0.805 | 0 |
| Syndig1l | 0 | -0.5406834 | 0.559 | 0.726 | 0 |
| Zkscan3 | 0 | 0.0640989 | 0.697 | 0.488 | 0 |
| Vmn1r209 | 0 | 1.3133292 | 0.552 | 0.364 | 0 |
| Fchsd2 | 0 | 0.1316013 | 0.752 | 0.534 | 0 |
| Vmn1r87 | 0 | 0.6492669 | 0.775 | 0.605 | 0 |
| Foxp2 | 0 | 0.7990055 | 0.607 | 0.434 | 0 |
| Eif2ak2 | 0 | -0.3034954 | 0.696 | 0.494 | 0 |
| Or1l4 | 0 | 0.6202373 | 0.690 | 0.518 | 0 |
| Or52e19 | 0 | 1.4995549 | 0.401 | 0.217 | 0 |
| Mrpl48 | 0 | -0.1820045 | 0.683 | 0.497 | 0 |
| Pkib | 0 | 0.2775215 | 0.786 | 0.599 | 0 |
| Haus8 | 0 | 0.4061894 | 0.757 | 0.594 | 0 |
| Zfp729a | 0 | 0.0280478 | 0.574 | 0.375 | 0 |
Microglia0_vs_Microglia1_comorbid
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-5.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Trac | 0 | -1.7063491 | 0.660 | 0.869 | 0 |
| Arfgef3 | 0 | -1.0887626 | 0.665 | 0.874 | 0 |
| Vmn1r218 | 0 | 0.8801728 | 0.898 | 0.717 | 0 |
| Cpa6 | 0 | 1.3559398 | 0.760 | 0.522 | 0 |
| Lipe | 0 | -1.1115953 | 0.851 | 0.935 | 0 |
| Or4f14b | 0 | 0.9868262 | 0.956 | 0.832 | 0 |
| Or51q1 | 0 | 0.8486383 | 0.922 | 0.778 | 0 |
| Vmn1r201 | 0 | 1.8546872 | 0.588 | 0.344 | 0 |
| Fgd4 | 0 | 0.4592167 | 0.933 | 0.805 | 0 |
| Vmn1r76 | 0 | 1.3102043 | 0.810 | 0.615 | 0 |
| Or13a17 | 0 | 0.5632069 | 0.797 | 0.593 | 0 |
| Vmn1r81 | 0 | 1.0998458 | 0.935 | 0.791 | 0 |
| Or1f19 | 0 | 1.1797206 | 0.800 | 0.603 | 0 |
| Vmn1r6 | 0 | 1.0752258 | 0.739 | 0.533 | 0 |
| Or6z3 | 0 | 0.8587296 | 0.901 | 0.741 | 0 |
| Psg16 | 0 | 0.8487776 | 0.820 | 0.605 | 0 |
| Cyb5r4 | 0 | 0.8345815 | 0.733 | 0.529 | 0 |
| Nipal2 | 0 | 0.7547669 | 0.817 | 0.630 | 0 |
| Or13a18 | 0 | 0.7794006 | 0.844 | 0.701 | 0 |
| Slc38a6 | 0 | 0.6364006 | 0.893 | 0.718 | 0 |
| Sik2 | 0 | 0.5163416 | 0.878 | 0.708 | 0 |
| Or13a25 | 0 | 0.8214713 | 0.767 | 0.552 | 0 |
| Traf5 | 0 | 0.3551980 | 0.794 | 0.608 | 0 |
| Snhg14 | 0 | 1.0264191 | 0.911 | 0.762 | 0 |
| Or6c6c | 0 | 0.6616574 | 0.723 | 0.507 | 0 |
| Zfp369 | 0 | 0.4648512 | 0.871 | 0.666 | 0 |
| Sros1 | 0 | 0.8076862 | 0.812 | 0.646 | 0 |
| Vmn1r197 | 0 | 1.2872492 | 0.785 | 0.611 | 0 |
| Cep112it | 0 | 1.0929949 | 0.611 | 0.395 | 0 |
| Or6c8 | 0 | 1.5051352 | 0.669 | 0.462 | 0 |
| Cux2 | 0 | -0.9025422 | 0.808 | 0.924 | 0 |
| Prdm11 | 0 | 0.4472788 | 0.614 | 0.385 | 0 |
| Acad9 | 0 | 0.4533341 | 0.787 | 0.612 | 0 |
| Hsd3b2 | 0 | 1.9297267 | 0.635 | 0.442 | 0 |
| Cul4a | 0 | 0.7300919 | 0.729 | 0.547 | 0 |
| Slfn3 | 0 | 0.5367422 | 0.700 | 0.483 | 0 |
| Eif2a | 0 | -0.7878757 | 0.865 | 0.937 | 0 |
| Or10ag54 | 0 | 0.8337652 | 0.820 | 0.650 | 0 |
| Vmn1r46 | 0 | 0.8794171 | 0.794 | 0.602 | 0 |
| Or10h28 | 0 | 0.7131371 | 0.790 | 0.615 | 0 |
| Nopchap1 | 0 | 0.8011462 | 0.986 | 0.934 | 0 |
| Vmn1r18 | 0 | 1.1206616 | 0.776 | 0.596 | 0 |
| Or52k2 | 0 | 0.8714795 | 0.703 | 0.523 | 0 |
| Or1ab2 | 0 | 0.9178200 | 0.773 | 0.586 | 0 |
| Maip1 | 0 | 0.5767887 | 0.650 | 0.447 | 0 |
| Or4a77 | 0 | 1.4103791 | 0.671 | 0.458 | 0 |
| Or1j15 | 0 | 0.9185293 | 0.849 | 0.723 | 0 |
| Or51k1 | 0 | 1.1480351 | 0.812 | 0.667 | 0 |
| Vmn1r58 | 0 | 0.8989285 | 0.767 | 0.576 | 0 |
| Pax6 | 0 | -0.9621078 | 0.720 | 0.846 | 0 |
| Tmcc1 | 0 | 0.3037596 | 0.914 | 0.797 | 0 |
| Or4c115 | 0 | 1.3483142 | 0.591 | 0.390 | 0 |
| Bltp1 | 0 | 0.5276250 | 0.713 | 0.506 | 0 |
| Grip2 | 0 | 1.4998994 | 0.881 | 0.777 | 0 |
| Senp7 | 0 | 0.3728211 | 0.830 | 0.671 | 0 |
| Grk4 | 0 | 0.6580214 | 0.807 | 0.642 | 0 |
| Lars2 | 0 | -0.2339387 | 0.833 | 0.682 | 0 |
| Ucp2 | 0 | 0.7092400 | 0.421 | 0.210 | 0 |
| Kcnq1ot1 | 0 | 0.4429731 | 0.971 | 0.907 | 0 |
| Or6c208 | 0 | 1.0712086 | 0.675 | 0.479 | 0 |
| Or52m1 | 0 | -1.4214082 | 0.659 | 0.807 | 0 |
| 9930111J21Rik2 | 0 | 0.2874189 | 0.918 | 0.768 | 0 |
| Or7g23 | 0 | 0.7463336 | 0.740 | 0.591 | 0 |
| Ranbp3l | 0 | 0.8859967 | 0.735 | 0.532 | 0 |
| Cep290 | 0 | -0.9642513 | 0.828 | 0.916 | 0 |
| Ccdc82 | 0 | 0.7570261 | 0.717 | 0.542 | 0 |
| St14 | 0 | 0.6868633 | 0.671 | 0.471 | 0 |
| Nox4 | 0 | 0.4297913 | 0.600 | 0.370 | 0 |
| Ift20 | 0 | -0.7147168 | 0.729 | 0.872 | 0 |
| Zfp65 | 0 | 0.5765027 | 0.545 | 0.349 | 0 |
| Lpl | 0 | 0.3464301 | 0.739 | 0.541 | 0 |
| Rrm1 | 0 | 0.2793334 | 0.721 | 0.543 | 0 |
| Or5b124 | 0 | 0.9798651 | 0.686 | 0.534 | 0 |
| Nom1 | 0 | 0.7170819 | 0.793 | 0.617 | 0 |
| Bora | 0 | 0.5744559 | 0.504 | 0.307 | 0 |
| Pign | 0 | 0.4839414 | 0.810 | 0.631 | 0 |
| Vmn1r72 | 0 | 0.7085967 | 0.716 | 0.537 | 0 |
| Dpf1 | 0 | -0.7708053 | 0.531 | 0.682 | 0 |
| Macrod2os1 | 0 | 0.8181883 | 0.522 | 0.327 | 0 |
| Pi15 | 0 | 0.9551680 | 0.636 | 0.442 | 0 |
| Cflar | 0 | 0.1832956 | 0.827 | 0.677 | 0 |
| Glrx2 | 0 | 0.3575157 | 0.751 | 0.572 | 0 |
| Ncf2 | 0 | 0.3230060 | 0.720 | 0.523 | 0 |
| Zfp738 | 0 | 0.4564973 | 0.831 | 0.667 | 0 |
| Cnpy3 | 0 | 0.6840410 | 0.550 | 0.347 | 0 |
| Or4p4 | 0 | 0.9283994 | 0.733 | 0.548 | 0 |
| mt-Tq | 0 | -1.4433784 | 0.689 | 0.805 | 0 |
| Syndig1l | 0 | -0.5406834 | 0.559 | 0.726 | 0 |
| Zkscan3 | 0 | 0.0640989 | 0.697 | 0.488 | 0 |
| Vmn1r209 | 0 | 1.3133292 | 0.552 | 0.364 | 0 |
| Fchsd2 | 0 | 0.1316013 | 0.752 | 0.534 | 0 |
| Vmn1r87 | 0 | 0.6492669 | 0.775 | 0.605 | 0 |
| Foxp2 | 0 | 0.7990055 | 0.607 | 0.434 | 0 |
| Eif2ak2 | 0 | -0.3034954 | 0.696 | 0.494 | 0 |
| Or1l4 | 0 | 0.6202373 | 0.690 | 0.518 | 0 |
| Or52e19 | 0 | 1.4995549 | 0.401 | 0.217 | 0 |
| Mrpl48 | 0 | -0.1820045 | 0.683 | 0.497 | 0 |
| Pkib | 0 | 0.2775215 | 0.786 | 0.599 | 0 |
| Haus8 | 0 | 0.4061894 | 0.757 | 0.594 | 0 |
| Zfp729a | 0 | 0.0280478 | 0.574 | 0.375 | 0 |
Microglia0_vs_Microglia2
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-8.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Cst7 | 0 | -3.9686104 | 0.141 | 0.705 | 0 |
| Apoe | 0 | -2.6506012 | 0.616 | 0.937 | 0 |
| Clec7a | 0 | -2.8912634 | 0.138 | 0.668 | 0 |
| Ccl3 | 0 | -4.3531509 | 0.093 | 0.533 | 0 |
| Lyz2 | 0 | -1.9620885 | 0.636 | 0.921 | 0 |
| Ctsb | 0 | -1.2553728 | 0.965 | 0.993 | 0 |
| P2ry12 | 0 | 1.3417683 | 0.976 | 0.915 | 0 |
| Axl | 0 | -2.6048608 | 0.106 | 0.533 | 0 |
| Fth1 | 0 | -1.1728108 | 0.952 | 0.983 | 0 |
| Ctsz | 0 | -1.1364535 | 0.951 | 0.987 | 0 |
| Ftl1 | 0 | -1.0845956 | 0.948 | 0.976 | 0 |
| B2m | 0 | -0.8841796 | 0.984 | 0.989 | 0 |
| Ccl4 | 0 | -5.4590391 | 0.041 | 0.332 | 0 |
| Tmem119 | 0 | 1.3086498 | 0.951 | 0.760 | 0 |
| Cd63 | 0 | -1.5218787 | 0.675 | 0.893 | 0 |
| Ctsd | 0 | -1.0327399 | 0.996 | 1.000 | 0 |
| Lilrb4a | 0 | -4.0914589 | 0.050 | 0.345 | 0 |
| Selplg | 0 | 0.9323382 | 0.982 | 0.924 | 0 |
| Baiap2l2 | 0 | -3.2808146 | 0.015 | 0.238 | 0 |
| Serinc3 | 0 | 0.7581640 | 0.984 | 0.976 | 0 |
| Eef1a1 | 0 | -0.9604677 | 0.946 | 0.989 | 0 |
| Cox6a2 | 0 | -3.6852880 | 0.034 | 0.282 | 0 |
| Cd9 | 0 | -1.0278271 | 0.918 | 0.969 | 0 |
| Mif | 0 | -1.8511946 | 0.237 | 0.605 | 0 |
| Tyrobp | 0 | -1.2701819 | 0.950 | 0.980 | 0 |
| Npc2 | 0 | -1.1582156 | 0.805 | 0.926 | 0 |
| Rpl41 | 0 | -1.2166273 | 0.773 | 0.930 | 0 |
| Ank | 0 | -2.5357887 | 0.150 | 0.467 | 0 |
| Cx3cr1 | 0 | 0.8703880 | 0.992 | 0.972 | 0 |
| Lgals3bp | 0 | -1.5832710 | 0.433 | 0.758 | 0 |
| Capg | 0 | -2.4097202 | 0.103 | 0.406 | 0 |
| Itgax | 0 | -3.3825661 | 0.045 | 0.286 | 0 |
| Malat1 | 0 | 0.5418416 | 0.992 | 0.952 | 0 |
| Cd74 | 0 | -2.4327293 | 0.130 | 0.443 | 0 |
| Rpl18a | 0 | -0.9815482 | 0.873 | 0.952 | 0 |
| Csf1 | 0 | -2.9261667 | 0.052 | 0.301 | 0 |
| Myo1e | 0 | -2.4967895 | 0.082 | 0.358 | 0 |
| Cd52 | 0 | -1.5075890 | 0.426 | 0.738 | 0 |
| Cd68 | 0 | -1.0343826 | 0.820 | 0.932 | 0 |
| Rpl35rt | 0 | -1.1885764 | 0.731 | 0.915 | 0 |
| Ccl6 | 0 | -2.4365684 | 0.277 | 0.587 | 0 |
| Ch25h | 0 | -4.4413136 | 0.015 | 0.201 | 0 |
| Ctsl | 0 | -1.0159982 | 0.924 | 0.969 | 0 |
| Ivns1abp | 0 | 1.2930563 | 0.888 | 0.731 | 0 |
| Gnas | 0 | -1.6204026 | 0.442 | 0.734 | 0 |
| Ctss | 0 | -0.4719540 | 0.995 | 1.000 | 0 |
| Hif1a | 0 | -1.5643552 | 0.262 | 0.587 | 0 |
| Rplp1 | 0 | -0.9466536 | 0.802 | 0.932 | 0 |
| Gapdh | 0 | -1.2885205 | 0.661 | 0.841 | 0 |
| Spp1 | 0 | -7.7962458 | 0.017 | 0.177 | 0 |
| Rpl21 | 0 | -1.1188142 | 0.636 | 0.856 | 0 |
| Rps28 | 0 | -1.0568365 | 0.701 | 0.891 | 0 |
| H2-D1 | 0 | -0.8545038 | 0.831 | 0.941 | 0 |
| Aldoa | 0 | -1.2316458 | 0.545 | 0.784 | 0 |
| Rpl35 | 0 | -1.0361363 | 0.760 | 0.928 | 0 |
| Rpl32 | 0 | -0.9739009 | 0.670 | 0.882 | 0 |
| Rps18 | 0 | -1.0264550 | 0.681 | 0.865 | 0 |
| Ramp1 | 0 | -2.0014110 | 0.123 | 0.380 | 0 |
| Serpine2 | 0 | -1.0954029 | 0.844 | 0.928 | 0 |
| Uba52 | 0 | -1.0300158 | 0.559 | 0.812 | 0 |
| Anxa5 | 0 | -1.9086755 | 0.131 | 0.389 | 0 |
| Cpd | 0 | -1.7734823 | 0.094 | 0.328 | 0 |
| Crlf2 | 0 | -1.6833915 | 0.099 | 0.338 | 0 |
| Nicol1 | 0 | -2.8912067 | 0.022 | 0.179 | 0 |
| Tpi1 | 0 | -1.5549716 | 0.174 | 0.441 | 0 |
| Rps16-ps2 | 0 | -1.2757444 | 0.430 | 0.701 | 0 |
| Mt1 | 0 | -1.1482896 | 0.276 | 0.594 | 0 |
| Wfdc17 | 0 | -3.4174334 | 0.010 | 0.140 | 0 |
| Ifi27l2a | 0 | -1.4590027 | 0.137 | 0.393 | 0 |
| Lpl | 0 | -3.0948877 | 0.739 | 0.825 | 0 |
| Rpl37a | 0 | -0.9054676 | 0.697 | 0.865 | 0 |
| Maf | 0 | 1.1640231 | 0.856 | 0.688 | 0 |
| Zfp691 | 0 | 1.3945194 | 0.872 | 0.758 | 0 |
| Tpt1 | 0 | -1.1415396 | 0.618 | 0.825 | 0 |
| Rps19 | 0 | -0.9052618 | 0.703 | 0.871 | 0 |
| Plaur | 0 | -2.6550672 | 0.085 | 0.290 | 0 |
| Csf1r | 0 | 0.4878526 | 0.991 | 0.991 | 0 |
| Rpl10a | 0 | -0.8873125 | 0.554 | 0.801 | 0 |
| Rpl13a | 0 | -0.8099290 | 0.766 | 0.917 | 0 |
| Psat1 | 0 | -1.6504466 | 0.090 | 0.308 | 0 |
| Rps2 | 0 | -1.0354959 | 0.541 | 0.786 | 0 |
| P2ry13 | 0 | 1.1115332 | 0.837 | 0.701 | 0 |
| Uba52rt | 0 | -1.0465813 | 0.507 | 0.755 | 0 |
| Srgap2 | 0 | 1.1662103 | 0.837 | 0.638 | 0 |
| Rplp0 | 0 | -0.9526933 | 0.703 | 0.852 | 0 |
| Or5v1 | 0 | -4.0127099 | 0.035 | 0.197 | 0 |
| Igf1 | 0 | -3.0129862 | 0.149 | 0.367 | 0 |
| Rpl23a | 0 | -1.1078486 | 0.396 | 0.686 | 0 |
| Dpp7 | 0 | -1.4386560 | 0.124 | 0.358 | 0 |
| Aplp2 | 0 | -1.4008564 | 0.181 | 0.434 | 0 |
| Pkm | 0 | -1.3137763 | 0.382 | 0.642 | 0 |
| Nceh1 | 0 | -1.8755664 | 0.113 | 0.328 | 0 |
| Rps23-ps1 | 0 | -0.8477680 | 0.649 | 0.841 | 0 |
| Fam20c | 0 | -2.6731972 | 0.055 | 0.227 | 0 |
| Rps15 | 0 | -1.1834704 | 0.498 | 0.725 | 0 |
| Cd83 | 0 | -1.5924008 | 0.363 | 0.629 | 0 |
| Pld3 | 0 | -1.2727364 | 0.294 | 0.557 | 0 |
| Crip1 | 0 | -2.5825650 | 0.084 | 0.273 | 0 |
| Ftl1-ps1 | 0 | -0.6357664 | 0.615 | 0.779 | 0 |
| Rps29 | 0 | -0.7011352 | 0.886 | 0.961 | 0 |
Microglia0_vs_Microglia2_comorbid
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-11.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Cst7 | 0 | -3.9686104 | 0.141 | 0.705 | 0 |
| Apoe | 0 | -2.6506012 | 0.616 | 0.937 | 0 |
| Clec7a | 0 | -2.8912634 | 0.138 | 0.668 | 0 |
| Ccl3 | 0 | -4.3531509 | 0.093 | 0.533 | 0 |
| Lyz2 | 0 | -1.9620885 | 0.636 | 0.921 | 0 |
| Ctsb | 0 | -1.2553728 | 0.965 | 0.993 | 0 |
| P2ry12 | 0 | 1.3417683 | 0.976 | 0.915 | 0 |
| Axl | 0 | -2.6048608 | 0.106 | 0.533 | 0 |
| Fth1 | 0 | -1.1728108 | 0.952 | 0.983 | 0 |
| Ctsz | 0 | -1.1364535 | 0.951 | 0.987 | 0 |
| Ftl1 | 0 | -1.0845956 | 0.948 | 0.976 | 0 |
| B2m | 0 | -0.8841796 | 0.984 | 0.989 | 0 |
| Ccl4 | 0 | -5.4590391 | 0.041 | 0.332 | 0 |
| Tmem119 | 0 | 1.3086498 | 0.951 | 0.760 | 0 |
| Cd63 | 0 | -1.5218787 | 0.675 | 0.893 | 0 |
| Ctsd | 0 | -1.0327399 | 0.996 | 1.000 | 0 |
| Lilrb4a | 0 | -4.0914589 | 0.050 | 0.345 | 0 |
| Selplg | 0 | 0.9323382 | 0.982 | 0.924 | 0 |
| Baiap2l2 | 0 | -3.2808146 | 0.015 | 0.238 | 0 |
| Serinc3 | 0 | 0.7581640 | 0.984 | 0.976 | 0 |
| Eef1a1 | 0 | -0.9604677 | 0.946 | 0.989 | 0 |
| Cox6a2 | 0 | -3.6852880 | 0.034 | 0.282 | 0 |
| Cd9 | 0 | -1.0278271 | 0.918 | 0.969 | 0 |
| Mif | 0 | -1.8511946 | 0.237 | 0.605 | 0 |
| Tyrobp | 0 | -1.2701819 | 0.950 | 0.980 | 0 |
| Npc2 | 0 | -1.1582156 | 0.805 | 0.926 | 0 |
| Rpl41 | 0 | -1.2166273 | 0.773 | 0.930 | 0 |
| Ank | 0 | -2.5357887 | 0.150 | 0.467 | 0 |
| Cx3cr1 | 0 | 0.8703880 | 0.992 | 0.972 | 0 |
| Lgals3bp | 0 | -1.5832710 | 0.433 | 0.758 | 0 |
| Capg | 0 | -2.4097202 | 0.103 | 0.406 | 0 |
| Itgax | 0 | -3.3825661 | 0.045 | 0.286 | 0 |
| Malat1 | 0 | 0.5418416 | 0.992 | 0.952 | 0 |
| Cd74 | 0 | -2.4327293 | 0.130 | 0.443 | 0 |
| Rpl18a | 0 | -0.9815482 | 0.873 | 0.952 | 0 |
| Csf1 | 0 | -2.9261667 | 0.052 | 0.301 | 0 |
| Myo1e | 0 | -2.4967895 | 0.082 | 0.358 | 0 |
| Cd52 | 0 | -1.5075890 | 0.426 | 0.738 | 0 |
| Cd68 | 0 | -1.0343826 | 0.820 | 0.932 | 0 |
| Rpl35rt | 0 | -1.1885764 | 0.731 | 0.915 | 0 |
| Ccl6 | 0 | -2.4365684 | 0.277 | 0.587 | 0 |
| Ch25h | 0 | -4.4413136 | 0.015 | 0.201 | 0 |
| Ctsl | 0 | -1.0159982 | 0.924 | 0.969 | 0 |
| Ivns1abp | 0 | 1.2930563 | 0.888 | 0.731 | 0 |
| Gnas | 0 | -1.6204026 | 0.442 | 0.734 | 0 |
| Ctss | 0 | -0.4719540 | 0.995 | 1.000 | 0 |
| Hif1a | 0 | -1.5643552 | 0.262 | 0.587 | 0 |
| Rplp1 | 0 | -0.9466536 | 0.802 | 0.932 | 0 |
| Gapdh | 0 | -1.2885205 | 0.661 | 0.841 | 0 |
| Spp1 | 0 | -7.7962458 | 0.017 | 0.177 | 0 |
| Rpl21 | 0 | -1.1188142 | 0.636 | 0.856 | 0 |
| Rps28 | 0 | -1.0568365 | 0.701 | 0.891 | 0 |
| H2-D1 | 0 | -0.8545038 | 0.831 | 0.941 | 0 |
| Aldoa | 0 | -1.2316458 | 0.545 | 0.784 | 0 |
| Rpl35 | 0 | -1.0361363 | 0.760 | 0.928 | 0 |
| Rpl32 | 0 | -0.9739009 | 0.670 | 0.882 | 0 |
| Rps18 | 0 | -1.0264550 | 0.681 | 0.865 | 0 |
| Ramp1 | 0 | -2.0014110 | 0.123 | 0.380 | 0 |
| Serpine2 | 0 | -1.0954029 | 0.844 | 0.928 | 0 |
| Uba52 | 0 | -1.0300158 | 0.559 | 0.812 | 0 |
| Anxa5 | 0 | -1.9086755 | 0.131 | 0.389 | 0 |
| Cpd | 0 | -1.7734823 | 0.094 | 0.328 | 0 |
| Crlf2 | 0 | -1.6833915 | 0.099 | 0.338 | 0 |
| Nicol1 | 0 | -2.8912067 | 0.022 | 0.179 | 0 |
| Tpi1 | 0 | -1.5549716 | 0.174 | 0.441 | 0 |
| Rps16-ps2 | 0 | -1.2757444 | 0.430 | 0.701 | 0 |
| Mt1 | 0 | -1.1482896 | 0.276 | 0.594 | 0 |
| Wfdc17 | 0 | -3.4174334 | 0.010 | 0.140 | 0 |
| Ifi27l2a | 0 | -1.4590027 | 0.137 | 0.393 | 0 |
| Lpl | 0 | -3.0948877 | 0.739 | 0.825 | 0 |
| Rpl37a | 0 | -0.9054676 | 0.697 | 0.865 | 0 |
| Maf | 0 | 1.1640231 | 0.856 | 0.688 | 0 |
| Zfp691 | 0 | 1.3945194 | 0.872 | 0.758 | 0 |
| Tpt1 | 0 | -1.1415396 | 0.618 | 0.825 | 0 |
| Rps19 | 0 | -0.9052618 | 0.703 | 0.871 | 0 |
| Plaur | 0 | -2.6550672 | 0.085 | 0.290 | 0 |
| Csf1r | 0 | 0.4878526 | 0.991 | 0.991 | 0 |
| Rpl10a | 0 | -0.8873125 | 0.554 | 0.801 | 0 |
| Rpl13a | 0 | -0.8099290 | 0.766 | 0.917 | 0 |
| Psat1 | 0 | -1.6504466 | 0.090 | 0.308 | 0 |
| Rps2 | 0 | -1.0354959 | 0.541 | 0.786 | 0 |
| P2ry13 | 0 | 1.1115332 | 0.837 | 0.701 | 0 |
| Uba52rt | 0 | -1.0465813 | 0.507 | 0.755 | 0 |
| Srgap2 | 0 | 1.1662103 | 0.837 | 0.638 | 0 |
| Rplp0 | 0 | -0.9526933 | 0.703 | 0.852 | 0 |
| Or5v1 | 0 | -4.0127099 | 0.035 | 0.197 | 0 |
| Igf1 | 0 | -3.0129862 | 0.149 | 0.367 | 0 |
| Rpl23a | 0 | -1.1078486 | 0.396 | 0.686 | 0 |
| Dpp7 | 0 | -1.4386560 | 0.124 | 0.358 | 0 |
| Aplp2 | 0 | -1.4008564 | 0.181 | 0.434 | 0 |
| Pkm | 0 | -1.3137763 | 0.382 | 0.642 | 0 |
| Nceh1 | 0 | -1.8755664 | 0.113 | 0.328 | 0 |
| Rps23-ps1 | 0 | -0.8477680 | 0.649 | 0.841 | 0 |
| Fam20c | 0 | -2.6731972 | 0.055 | 0.227 | 0 |
| Rps15 | 0 | -1.1834704 | 0.498 | 0.725 | 0 |
| Cd83 | 0 | -1.5924008 | 0.363 | 0.629 | 0 |
| Pld3 | 0 | -1.2727364 | 0.294 | 0.557 | 0 |
| Crip1 | 0 | -2.5825650 | 0.084 | 0.273 | 0 |
| Ftl1-ps1 | 0 | -0.6357664 | 0.615 | 0.779 | 0 |
| Rps29 | 0 | -0.7011352 | 0.886 | 0.961 | 0 |
Microglia0_vs_Microglia3
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-14.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Rab3gap1 | 0 | 2.3200799 | 0.817 | 0.207 | 0 |
| Ctsd | 0 | 1.2598236 | 0.996 | 0.793 | 0 |
| Slc38a6 | 0 | 1.2312242 | 0.893 | 0.369 | 0 |
| Laptm5 | 0 | 1.2501469 | 0.982 | 0.665 | 0 |
| Ppp2r5a | 0 | 1.8225729 | 0.760 | 0.182 | 0 |
| Inpp5d | 0 | 0.7842893 | 0.879 | 0.355 | 0 |
| Lair1 | 0 | 1.2800298 | 0.892 | 0.429 | 0 |
| C1qa | 0 | 1.0980093 | 0.993 | 0.675 | 0 |
| C1qc | 0 | 1.1052075 | 0.991 | 0.729 | 0 |
| Olfml3 | 0 | 1.2549123 | 0.946 | 0.586 | 0 |
| Noct | 0 | 0.7950282 | 0.912 | 0.409 | 0 |
| Grn | 0 | 0.9498269 | 0.918 | 0.473 | 0 |
| Csf1r | 0 | 1.0462852 | 0.991 | 0.759 | 0 |
| H2-D1 | 0 | 1.5873462 | 0.831 | 0.355 | 0 |
| Pikfyve | 0 | 0.6056509 | 0.847 | 0.296 | 0 |
| Man2b1 | 0 | 0.8639139 | 0.875 | 0.399 | 0 |
| Eif2a | 0 | -3.7447815 | 0.865 | 0.941 | 0 |
| Serpine2 | 0 | 1.4775072 | 0.844 | 0.369 | 0 |
| Trac | 0 | -4.8542294 | 0.660 | 0.823 | 0 |
| Lipe | 0 | -3.8671953 | 0.851 | 0.975 | 0 |
| Pag1 | 0 | 2.2174891 | 0.702 | 0.192 | 0 |
| Scamp2 | 0 | 0.9552592 | 0.764 | 0.296 | 0 |
| Ctsh | 0 | 0.0368091 | 0.850 | 0.379 | 0 |
| Krit1 | 0 | 1.1593111 | 0.891 | 0.404 | 0 |
| Or13a17 | 0 | -0.2890799 | 0.797 | 0.266 | 0 |
| Cyth4 | 0 | 1.2490852 | 0.857 | 0.389 | 0 |
| Ctsz | 0 | 0.9088155 | 0.951 | 0.552 | 0 |
| Ctsb | 0 | 0.8587905 | 0.965 | 0.586 | 0 |
| Selenop | 0 | 0.7220140 | 0.941 | 0.512 | 0 |
| Ctsa | 0 | 0.6901389 | 0.925 | 0.502 | 0 |
| Or6c208 | 0 | 2.3131314 | 0.675 | 0.158 | 0 |
| Psap | 0 | 0.8289519 | 0.972 | 0.626 | 0 |
| Trem2 | 0 | 0.8711685 | 0.946 | 0.527 | 0 |
| Nrros | 0 | 0.4219785 | 0.762 | 0.261 | 0 |
| Cyb5r4 | 0 | 2.3305416 | 0.733 | 0.212 | 0 |
| Tmem119 | 0 | 1.0343938 | 0.951 | 0.576 | 0 |
| Ubc | 0 | 1.6796496 | 0.784 | 0.330 | 0 |
| Vmn1r13 | 0 | -4.5197170 | 0.834 | 0.946 | 0 |
| Sfi1 | 0 | 1.7410775 | 0.762 | 0.291 | 0 |
| Nom1 | 0 | 1.7834190 | 0.793 | 0.276 | 0 |
| Cd9 | 0 | 1.0201080 | 0.918 | 0.537 | 0 |
| Cpa6 | 0 | 1.0156069 | 0.760 | 0.217 | 0 |
| Unc93b1 | 0 | 0.7158821 | 0.861 | 0.365 | 0 |
| Ncf2 | 0 | 0.3044496 | 0.720 | 0.222 | 0 |
| Tmbim6 | 0 | 1.3931614 | 0.821 | 0.365 | 0 |
| Or10h28 | 0 | 0.6733835 | 0.790 | 0.256 | 0 |
| Frmd4a | 0 | 0.7927926 | 0.791 | 0.286 | 0 |
| Chd9 | 0 | 0.1745577 | 0.928 | 0.433 | 0 |
| Arhgef40 | 0 | 0.7038944 | 0.767 | 0.251 | 0 |
| Nav2 | 0 | 2.2942769 | 0.770 | 0.296 | 0 |
| Or52k2 | 0 | 1.6546740 | 0.703 | 0.202 | 0 |
| Fyco1 | 0 | 1.4918146 | 0.682 | 0.182 | 0 |
| Ifngr1 | 0 | 0.3134351 | 0.902 | 0.473 | 0 |
| Pld4 | 0 | 1.1002495 | 0.908 | 0.498 | 0 |
| Mef2c | 0 | 1.1774500 | 0.787 | 0.310 | 0 |
| Pkib | 0 | 1.7546664 | 0.786 | 0.296 | 0 |
| Dnajb14 | 0 | 2.0286524 | 0.668 | 0.177 | 0 |
| Pdia3 | 0 | 0.9873904 | 0.785 | 0.325 | 0 |
| Sirt5 | 0 | 1.1619146 | 0.804 | 0.330 | 0 |
| Cx3cr1 | 0 | 0.8751947 | 0.992 | 0.704 | 0 |
| Or1ab2 | 0 | 1.0569570 | 0.773 | 0.256 | 0 |
| Tmem234 | 0 | 2.5641863 | 0.696 | 0.212 | 0 |
| Rsrp1 | 0 | 0.6974994 | 0.924 | 0.468 | 0 |
| Fcgr3 | 0 | 0.4645940 | 0.968 | 0.567 | 0 |
| Nisch | 0 | 1.5046671 | 0.797 | 0.335 | 0 |
| Pan3 | 0 | 0.9867249 | 0.804 | 0.315 | 0 |
| Vmn1r76 | 0 | 1.4066831 | 0.810 | 0.300 | 0 |
| Vsir | 0 | 0.8326679 | 0.938 | 0.532 | 0 |
| Or13a18 | 0 | 0.5147844 | 0.844 | 0.350 | 0 |
| Stab1 | 0 | 1.4345018 | 0.820 | 0.399 | 0 |
| Csf3r | 0 | 1.5151226 | 0.794 | 0.330 | 0 |
| Bin1 | 0 | 0.5369929 | 0.729 | 0.227 | 0 |
| Selplg | 0 | 0.7874496 | 0.982 | 0.670 | 0 |
| Fth1 | 0 | 0.4950527 | 0.952 | 0.581 | 0 |
| Ubb | 0 | 0.5284641 | 0.936 | 0.394 | 0 |
| Ankrd17 | 0 | 1.4264851 | 0.730 | 0.261 | 0 |
| Arhgap45 | 0 | 0.9233148 | 0.785 | 0.315 | 0 |
| Acer3 | 0 | 1.6332087 | 0.772 | 0.296 | 0 |
| Grk4 | 0 | 0.3649651 | 0.807 | 0.286 | 0 |
| Hsp90b1 | 0 | 0.3003394 | 0.806 | 0.330 | 0 |
| Arfgef3 | 0 | -3.5194664 | 0.665 | 0.833 | 0 |
| Elmo1 | 0 | 1.6432982 | 0.733 | 0.286 | 0 |
| Ftl1 | 0 | 0.6317278 | 0.948 | 0.517 | 0 |
| St14 | 0 | 0.5687877 | 0.671 | 0.177 | 0 |
| Sirpa | 0 | 0.9579991 | 0.945 | 0.542 | 0 |
| Serinc3 | 0 | 0.6797207 | 0.984 | 0.714 | 0 |
| Atp6v0b | 0 | 1.2339277 | 0.760 | 0.291 | 0 |
| Fus | 0 | 1.3333049 | 0.778 | 0.335 | 0 |
| Vmn1r197 | 0 | 0.0319971 | 0.785 | 0.296 | 0 |
| Zfp738 | 0 | 0.5534946 | 0.831 | 0.345 | 0 |
| Or1f19 | 0 | 0.8493404 | 0.800 | 0.305 | 0 |
| Acad9 | 0 | 0.9169148 | 0.787 | 0.281 | 0 |
| Pign | 0 | -0.1385837 | 0.810 | 0.315 | 0 |
| Ly86 | 0 | 0.4635936 | 0.942 | 0.512 | 0 |
| Lpcat2 | 0 | 0.4304866 | 0.909 | 0.463 | 0 |
| Ppcdc | 0 | 0.5652759 | 0.796 | 0.369 | 0 |
| Tgfbr1 | 0 | 0.3172245 | 0.960 | 0.571 | 0 |
| Tyrobp | 0 | 0.9098924 | 0.950 | 0.562 | 0 |
| Cux2 | 0 | -3.7026818 | 0.808 | 0.906 | 0 |
| Rbm25 | 0 | 0.3370216 | 0.850 | 0.394 | 0 |
Microglia0_vs_Microglia3_comorbid
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-17.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Rab3gap1 | 0 | 2.3200799 | 0.817 | 0.207 | 0 |
| Ctsd | 0 | 1.2598236 | 0.996 | 0.793 | 0 |
| Slc38a6 | 0 | 1.2312242 | 0.893 | 0.369 | 0 |
| Laptm5 | 0 | 1.2501469 | 0.982 | 0.665 | 0 |
| Ppp2r5a | 0 | 1.8225729 | 0.760 | 0.182 | 0 |
| Inpp5d | 0 | 0.7842893 | 0.879 | 0.355 | 0 |
| Lair1 | 0 | 1.2800298 | 0.892 | 0.429 | 0 |
| C1qa | 0 | 1.0980093 | 0.993 | 0.675 | 0 |
| C1qc | 0 | 1.1052075 | 0.991 | 0.729 | 0 |
| Olfml3 | 0 | 1.2549123 | 0.946 | 0.586 | 0 |
| Noct | 0 | 0.7950282 | 0.912 | 0.409 | 0 |
| Grn | 0 | 0.9498269 | 0.918 | 0.473 | 0 |
| Csf1r | 0 | 1.0462852 | 0.991 | 0.759 | 0 |
| H2-D1 | 0 | 1.5873462 | 0.831 | 0.355 | 0 |
| Pikfyve | 0 | 0.6056509 | 0.847 | 0.296 | 0 |
| Man2b1 | 0 | 0.8639139 | 0.875 | 0.399 | 0 |
| Eif2a | 0 | -3.7447815 | 0.865 | 0.941 | 0 |
| Serpine2 | 0 | 1.4775072 | 0.844 | 0.369 | 0 |
| Trac | 0 | -4.8542294 | 0.660 | 0.823 | 0 |
| Lipe | 0 | -3.8671953 | 0.851 | 0.975 | 0 |
| Pag1 | 0 | 2.2174891 | 0.702 | 0.192 | 0 |
| Scamp2 | 0 | 0.9552592 | 0.764 | 0.296 | 0 |
| Ctsh | 0 | 0.0368091 | 0.850 | 0.379 | 0 |
| Krit1 | 0 | 1.1593111 | 0.891 | 0.404 | 0 |
| Or13a17 | 0 | -0.2890799 | 0.797 | 0.266 | 0 |
| Cyth4 | 0 | 1.2490852 | 0.857 | 0.389 | 0 |
| Ctsz | 0 | 0.9088155 | 0.951 | 0.552 | 0 |
| Ctsb | 0 | 0.8587905 | 0.965 | 0.586 | 0 |
| Selenop | 0 | 0.7220140 | 0.941 | 0.512 | 0 |
| Ctsa | 0 | 0.6901389 | 0.925 | 0.502 | 0 |
| Or6c208 | 0 | 2.3131314 | 0.675 | 0.158 | 0 |
| Psap | 0 | 0.8289519 | 0.972 | 0.626 | 0 |
| Trem2 | 0 | 0.8711685 | 0.946 | 0.527 | 0 |
| Nrros | 0 | 0.4219785 | 0.762 | 0.261 | 0 |
| Cyb5r4 | 0 | 2.3305416 | 0.733 | 0.212 | 0 |
| Tmem119 | 0 | 1.0343938 | 0.951 | 0.576 | 0 |
| Ubc | 0 | 1.6796496 | 0.784 | 0.330 | 0 |
| Vmn1r13 | 0 | -4.5197170 | 0.834 | 0.946 | 0 |
| Sfi1 | 0 | 1.7410775 | 0.762 | 0.291 | 0 |
| Nom1 | 0 | 1.7834190 | 0.793 | 0.276 | 0 |
| Cd9 | 0 | 1.0201080 | 0.918 | 0.537 | 0 |
| Cpa6 | 0 | 1.0156069 | 0.760 | 0.217 | 0 |
| Unc93b1 | 0 | 0.7158821 | 0.861 | 0.365 | 0 |
| Ncf2 | 0 | 0.3044496 | 0.720 | 0.222 | 0 |
| Tmbim6 | 0 | 1.3931614 | 0.821 | 0.365 | 0 |
| Or10h28 | 0 | 0.6733835 | 0.790 | 0.256 | 0 |
| Frmd4a | 0 | 0.7927926 | 0.791 | 0.286 | 0 |
| Chd9 | 0 | 0.1745577 | 0.928 | 0.433 | 0 |
| Arhgef40 | 0 | 0.7038944 | 0.767 | 0.251 | 0 |
| Nav2 | 0 | 2.2942769 | 0.770 | 0.296 | 0 |
| Or52k2 | 0 | 1.6546740 | 0.703 | 0.202 | 0 |
| Fyco1 | 0 | 1.4918146 | 0.682 | 0.182 | 0 |
| Ifngr1 | 0 | 0.3134351 | 0.902 | 0.473 | 0 |
| Pld4 | 0 | 1.1002495 | 0.908 | 0.498 | 0 |
| Mef2c | 0 | 1.1774500 | 0.787 | 0.310 | 0 |
| Pkib | 0 | 1.7546664 | 0.786 | 0.296 | 0 |
| Dnajb14 | 0 | 2.0286524 | 0.668 | 0.177 | 0 |
| Pdia3 | 0 | 0.9873904 | 0.785 | 0.325 | 0 |
| Sirt5 | 0 | 1.1619146 | 0.804 | 0.330 | 0 |
| Cx3cr1 | 0 | 0.8751947 | 0.992 | 0.704 | 0 |
| Or1ab2 | 0 | 1.0569570 | 0.773 | 0.256 | 0 |
| Tmem234 | 0 | 2.5641863 | 0.696 | 0.212 | 0 |
| Rsrp1 | 0 | 0.6974994 | 0.924 | 0.468 | 0 |
| Fcgr3 | 0 | 0.4645940 | 0.968 | 0.567 | 0 |
| Nisch | 0 | 1.5046671 | 0.797 | 0.335 | 0 |
| Pan3 | 0 | 0.9867249 | 0.804 | 0.315 | 0 |
| Vmn1r76 | 0 | 1.4066831 | 0.810 | 0.300 | 0 |
| Vsir | 0 | 0.8326679 | 0.938 | 0.532 | 0 |
| Or13a18 | 0 | 0.5147844 | 0.844 | 0.350 | 0 |
| Stab1 | 0 | 1.4345018 | 0.820 | 0.399 | 0 |
| Csf3r | 0 | 1.5151226 | 0.794 | 0.330 | 0 |
| Bin1 | 0 | 0.5369929 | 0.729 | 0.227 | 0 |
| Selplg | 0 | 0.7874496 | 0.982 | 0.670 | 0 |
| Fth1 | 0 | 0.4950527 | 0.952 | 0.581 | 0 |
| Ubb | 0 | 0.5284641 | 0.936 | 0.394 | 0 |
| Ankrd17 | 0 | 1.4264851 | 0.730 | 0.261 | 0 |
| Arhgap45 | 0 | 0.9233148 | 0.785 | 0.315 | 0 |
| Acer3 | 0 | 1.6332087 | 0.772 | 0.296 | 0 |
| Grk4 | 0 | 0.3649651 | 0.807 | 0.286 | 0 |
| Hsp90b1 | 0 | 0.3003394 | 0.806 | 0.330 | 0 |
| Arfgef3 | 0 | -3.5194664 | 0.665 | 0.833 | 0 |
| Elmo1 | 0 | 1.6432982 | 0.733 | 0.286 | 0 |
| Ftl1 | 0 | 0.6317278 | 0.948 | 0.517 | 0 |
| St14 | 0 | 0.5687877 | 0.671 | 0.177 | 0 |
| Sirpa | 0 | 0.9579991 | 0.945 | 0.542 | 0 |
| Serinc3 | 0 | 0.6797207 | 0.984 | 0.714 | 0 |
| Atp6v0b | 0 | 1.2339277 | 0.760 | 0.291 | 0 |
| Fus | 0 | 1.3333049 | 0.778 | 0.335 | 0 |
| Vmn1r197 | 0 | 0.0319971 | 0.785 | 0.296 | 0 |
| Zfp738 | 0 | 0.5534946 | 0.831 | 0.345 | 0 |
| Or1f19 | 0 | 0.8493404 | 0.800 | 0.305 | 0 |
| Acad9 | 0 | 0.9169148 | 0.787 | 0.281 | 0 |
| Pign | 0 | -0.1385837 | 0.810 | 0.315 | 0 |
| Ly86 | 0 | 0.4635936 | 0.942 | 0.512 | 0 |
| Lpcat2 | 0 | 0.4304866 | 0.909 | 0.463 | 0 |
| Ppcdc | 0 | 0.5652759 | 0.796 | 0.369 | 0 |
| Tgfbr1 | 0 | 0.3172245 | 0.960 | 0.571 | 0 |
| Tyrobp | 0 | 0.9098924 | 0.950 | 0.562 | 0 |
| Cux2 | 0 | -3.7026818 | 0.808 | 0.906 | 0 |
| Rbm25 | 0 | 0.3370216 | 0.850 | 0.394 | 0 |
Microglia0_vs_Microglia4
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Ifit3 | 0e+00 | -6.7519510 | 0.043 | 0.628 | 0.0000000 |
| Ifit2 | 0e+00 | -6.2509895 | 0.022 | 0.425 | 0.0000000 |
| Ifi206 | 0e+00 | -6.6172676 | 0.012 | 0.319 | 0.0000000 |
| Rtp4 | 0e+00 | -3.2501944 | 0.123 | 0.717 | 0.0000000 |
| Oas2 | 0e+00 | -4.6557561 | 0.018 | 0.327 | 0.0000000 |
| Ifi207 | 0e+00 | -4.2776523 | 0.025 | 0.354 | 0.0000000 |
| Tgtp2 | 0e+00 | -5.0102542 | 0.036 | 0.389 | 0.0000000 |
| Ccl12 | 0e+00 | -4.8412153 | 0.163 | 0.690 | 0.0000000 |
| Ifitm3 | 0e+00 | -3.6660454 | 0.099 | 0.566 | 0.0000000 |
| Irf7 | 0e+00 | -4.2309015 | 0.040 | 0.398 | 0.0000000 |
| Oas1a | 0e+00 | -3.6459814 | 0.056 | 0.460 | 0.0000000 |
| Usp18 | 0e+00 | -4.1857036 | 0.079 | 0.504 | 0.0000000 |
| Ifi211 | 0e+00 | -6.6039944 | 0.018 | 0.283 | 0.0000000 |
| Oasl2 | 0e+00 | -5.1832898 | 0.204 | 0.673 | 0.0000000 |
| Ifit3b | 0e+00 | -6.7944699 | 0.100 | 0.504 | 0.0000000 |
| Oas1g | 0e+00 | -3.1817911 | 0.055 | 0.407 | 0.0000000 |
| Stat1 | 0e+00 | -2.9243892 | 0.333 | 0.823 | 0.0000000 |
| Iigp1 | 0e+00 | -5.8173255 | 0.134 | 0.558 | 0.0000000 |
| Nlrc5 | 0e+00 | -3.4188688 | 0.067 | 0.425 | 0.0000000 |
| Mx1 | 0e+00 | -4.9429243 | 0.131 | 0.522 | 0.0000000 |
| Zbp1 | 0e+00 | -4.9780860 | 0.056 | 0.363 | 0.0000000 |
| Ifi209 | 0e+00 | -4.0632897 | 0.106 | 0.469 | 0.0000000 |
| Ifi27l2a | 0e+00 | -2.6566757 | 0.137 | 0.540 | 0.0000000 |
| Phf11a | 0e+00 | -4.3457070 | 0.053 | 0.345 | 0.0000000 |
| Iigp1c | 0e+00 | -3.6423472 | 0.203 | 0.602 | 0.0000000 |
| Fgl2 | 0e+00 | -2.9639154 | 0.092 | 0.442 | 0.0000000 |
| Helz2 | 0e+00 | -3.9479252 | 0.015 | 0.195 | 0.0000000 |
| Ifit1 | 0e+00 | -7.8531147 | 0.072 | 0.363 | 0.0000000 |
| Samd9l | 0e+00 | -3.9798418 | 0.032 | 0.257 | 0.0000000 |
| Cmpk2 | 0e+00 | -4.6826237 | 0.009 | 0.159 | 0.0000000 |
| Mx2 | 0e+00 | -3.4230106 | 0.048 | 0.310 | 0.0000000 |
| Lgals3bp | 0e+00 | -2.0021198 | 0.433 | 0.814 | 0.0000000 |
| Phf11b | 0e+00 | -2.9683906 | 0.084 | 0.389 | 0.0000000 |
| Ifi204 | 0e+00 | -3.1791376 | 0.389 | 0.726 | 0.0000000 |
| Rnf213 | 0e+00 | -2.5455150 | 0.236 | 0.628 | 0.0000000 |
| Trex1 | 0e+00 | -2.0023779 | 0.203 | 0.575 | 0.0000000 |
| Rsad2 | 0e+00 | -5.7591202 | 0.070 | 0.319 | 0.0000000 |
| Trim30a | 0e+00 | -1.7869126 | 0.362 | 0.726 | 0.0000000 |
| Ifi205 | 0e+00 | -2.7641257 | 0.016 | 0.159 | 0.0000000 |
| Isg15 | 0e+00 | -4.1544408 | 0.173 | 0.460 | 0.0000000 |
| Trim30d | 0e+00 | -2.0439900 | 0.238 | 0.584 | 0.0000000 |
| Ifi213 | 0e+00 | -3.9631963 | 0.219 | 0.513 | 0.0000000 |
| Slfn2 | 0e+00 | -2.7613254 | 0.186 | 0.487 | 0.0000000 |
| Ifi47 | 0e+00 | -5.9605329 | 0.005 | 0.097 | 0.0000000 |
| Ccl2 | 0e+00 | -4.3963968 | 0.015 | 0.142 | 0.0000000 |
| Oasl1 | 0e+00 | -6.0440790 | 0.026 | 0.177 | 0.0000000 |
| Phf11d | 0e+00 | -2.6600679 | 0.158 | 0.442 | 0.0000000 |
| Ly6a | 0e+00 | -3.4065126 | 0.035 | 0.204 | 0.0000000 |
| Parp12 | 0e+00 | -1.8393088 | 0.137 | 0.416 | 0.0000000 |
| B2m | 0e+00 | -0.6968649 | 0.984 | 1.000 | 0.0000000 |
| Ifi208 | 0e+00 | -3.5788855 | 0.183 | 0.469 | 0.0000000 |
| Bst2 | 0e+00 | -1.8245625 | 0.263 | 0.558 | 0.0000000 |
| Isg20 | 0e+00 | -2.6790339 | 0.035 | 0.195 | 0.0000000 |
| Parp14 | 0e+00 | -2.5719671 | 0.257 | 0.531 | 0.0000000 |
| Herc6 | 0e+00 | -2.8622272 | 0.429 | 0.681 | 0.0000000 |
| Xaf1 | 0e+00 | -2.5040517 | 0.481 | 0.708 | 0.0000000 |
| Gbp9 | 0e+00 | -2.2293329 | 0.075 | 0.283 | 0.0000000 |
| Ddx60 | 0e+00 | -2.3006137 | 0.133 | 0.381 | 0.0000000 |
| Fcgr1 | 0e+00 | -1.1529893 | 0.634 | 0.850 | 0.0000000 |
| Tor3a | 0e+00 | -1.9524058 | 0.230 | 0.496 | 0.0000000 |
| Sp100 | 0e+00 | -2.7831339 | 0.375 | 0.611 | 0.0000000 |
| Tgtp1 | 0e+00 | -3.5557912 | 0.022 | 0.142 | 0.0000000 |
| Axl | 0e+00 | -2.0141459 | 0.106 | 0.327 | 0.0000000 |
| Etnk1 | 0e+00 | -1.3333396 | 0.288 | 0.575 | 0.0000001 |
| Gvin1 | 0e+00 | -1.9487476 | 0.297 | 0.593 | 0.0000004 |
| Slfn8 | 0e+00 | -1.9722130 | 0.439 | 0.673 | 0.0000006 |
| Irgm1 | 0e+00 | -2.4908527 | 0.340 | 0.549 | 0.0000007 |
| Ifih1 | 0e+00 | -2.2804736 | 0.163 | 0.381 | 0.0000012 |
| Ifi214 | 0e+00 | -2.5325909 | 0.216 | 0.451 | 0.0000025 |
| Ly6e | 0e+00 | -0.9653821 | 0.831 | 0.912 | 0.0000027 |
| Dhx58 | 0e+00 | -2.4560680 | 0.180 | 0.398 | 0.0000030 |
| Znfx1 | 0e+00 | -1.4570059 | 0.256 | 0.522 | 0.0000036 |
| Ctss | 0e+00 | -0.3802187 | 0.995 | 1.000 | 0.0000046 |
| Trim30c | 0e+00 | -4.9083411 | 0.013 | 0.097 | 0.0000080 |
| Slfn5 | 0e+00 | -3.0208370 | 0.527 | 0.717 | 0.0000101 |
| Parp9 | 0e+00 | -1.7350533 | 0.168 | 0.389 | 0.0000124 |
| Nampt | 0e+00 | -1.4538988 | 0.095 | 0.283 | 0.0000136 |
| Gvin3 | 0e+00 | -1.3339944 | 0.062 | 0.221 | 0.0000156 |
| Pml | 0e+00 | -1.9517895 | 0.133 | 0.336 | 0.0000183 |
| Gvin-ps7 | 0e+00 | -1.7278799 | 0.310 | 0.558 | 0.0000205 |
| Psmb8 | 0e+00 | -1.2938055 | 0.451 | 0.690 | 0.0000215 |
| H2-D1 | 0e+00 | -0.8769748 | 0.831 | 0.903 | 0.0000402 |
| Stk-ps2 | 0e+00 | -3.5651474 | 0.009 | 0.080 | 0.0000439 |
| Ifi35 | 0e+00 | -1.5238354 | 0.195 | 0.416 | 0.0000593 |
| Il18bp | 0e+00 | -4.9709430 | 0.015 | 0.097 | 0.0000633 |
| Gvin2 | 0e+00 | -1.8304393 | 0.338 | 0.593 | 0.0000734 |
| Uba7 | 0e+00 | -1.3748398 | 0.247 | 0.487 | 0.0001701 |
| Dtx3l | 0e+00 | -1.5000648 | 0.478 | 0.690 | 0.0002960 |
| Gbp2 | 0e+00 | -3.0519719 | 0.029 | 0.133 | 0.0003474 |
| Nmi | 0e+00 | -1.4919321 | 0.113 | 0.292 | 0.0004628 |
| H2-K1 | 0e+00 | -0.9577947 | 0.778 | 0.841 | 0.0004653 |
| Socs1 | 0e+00 | -2.0940465 | 0.022 | 0.115 | 0.0005418 |
| Epsti1 | 0e+00 | -1.7535665 | 0.141 | 0.336 | 0.0005803 |
| Sdc3 | 0e+00 | -1.5345282 | 0.116 | 0.292 | 0.0006269 |
| Csf1 | 1e-07 | -2.5333990 | 0.052 | 0.177 | 0.0009569 |
| Igtp | 1e-07 | -1.8254598 | 0.236 | 0.434 | 0.0010707 |
| Tcstv4 | 1e-07 | -2.7218314 | 0.028 | 0.124 | 0.0014691 |
| Ogfr | 1e-07 | -1.1826233 | 0.104 | 0.274 | 0.0015311 |
| Scimp | 1e-07 | -2.6625806 | 0.035 | 0.142 | 0.0017639 |
| P2ry12 | 3e-07 | 0.5307100 | 0.976 | 0.965 | 0.0044757 |
Microglia0_vs_Microglia4_comorbid
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Ifit3 | 0e+00 | -6.7519510 | 0.043 | 0.628 | 0.0000000 |
| Ifit2 | 0e+00 | -6.2509895 | 0.022 | 0.425 | 0.0000000 |
| Ifi206 | 0e+00 | -6.6172676 | 0.012 | 0.319 | 0.0000000 |
| Rtp4 | 0e+00 | -3.2501944 | 0.123 | 0.717 | 0.0000000 |
| Oas2 | 0e+00 | -4.6557561 | 0.018 | 0.327 | 0.0000000 |
| Ifi207 | 0e+00 | -4.2776523 | 0.025 | 0.354 | 0.0000000 |
| Tgtp2 | 0e+00 | -5.0102542 | 0.036 | 0.389 | 0.0000000 |
| Ccl12 | 0e+00 | -4.8412153 | 0.163 | 0.690 | 0.0000000 |
| Ifitm3 | 0e+00 | -3.6660454 | 0.099 | 0.566 | 0.0000000 |
| Irf7 | 0e+00 | -4.2309015 | 0.040 | 0.398 | 0.0000000 |
| Oas1a | 0e+00 | -3.6459814 | 0.056 | 0.460 | 0.0000000 |
| Usp18 | 0e+00 | -4.1857036 | 0.079 | 0.504 | 0.0000000 |
| Ifi211 | 0e+00 | -6.6039944 | 0.018 | 0.283 | 0.0000000 |
| Oasl2 | 0e+00 | -5.1832898 | 0.204 | 0.673 | 0.0000000 |
| Ifit3b | 0e+00 | -6.7944699 | 0.100 | 0.504 | 0.0000000 |
| Oas1g | 0e+00 | -3.1817911 | 0.055 | 0.407 | 0.0000000 |
| Stat1 | 0e+00 | -2.9243892 | 0.333 | 0.823 | 0.0000000 |
| Iigp1 | 0e+00 | -5.8173255 | 0.134 | 0.558 | 0.0000000 |
| Nlrc5 | 0e+00 | -3.4188688 | 0.067 | 0.425 | 0.0000000 |
| Mx1 | 0e+00 | -4.9429243 | 0.131 | 0.522 | 0.0000000 |
| Zbp1 | 0e+00 | -4.9780860 | 0.056 | 0.363 | 0.0000000 |
| Ifi209 | 0e+00 | -4.0632897 | 0.106 | 0.469 | 0.0000000 |
| Ifi27l2a | 0e+00 | -2.6566757 | 0.137 | 0.540 | 0.0000000 |
| Phf11a | 0e+00 | -4.3457070 | 0.053 | 0.345 | 0.0000000 |
| Iigp1c | 0e+00 | -3.6423472 | 0.203 | 0.602 | 0.0000000 |
| Fgl2 | 0e+00 | -2.9639154 | 0.092 | 0.442 | 0.0000000 |
| Helz2 | 0e+00 | -3.9479252 | 0.015 | 0.195 | 0.0000000 |
| Ifit1 | 0e+00 | -7.8531147 | 0.072 | 0.363 | 0.0000000 |
| Samd9l | 0e+00 | -3.9798418 | 0.032 | 0.257 | 0.0000000 |
| Cmpk2 | 0e+00 | -4.6826237 | 0.009 | 0.159 | 0.0000000 |
| Mx2 | 0e+00 | -3.4230106 | 0.048 | 0.310 | 0.0000000 |
| Lgals3bp | 0e+00 | -2.0021198 | 0.433 | 0.814 | 0.0000000 |
| Phf11b | 0e+00 | -2.9683906 | 0.084 | 0.389 | 0.0000000 |
| Ifi204 | 0e+00 | -3.1791376 | 0.389 | 0.726 | 0.0000000 |
| Rnf213 | 0e+00 | -2.5455150 | 0.236 | 0.628 | 0.0000000 |
| Trex1 | 0e+00 | -2.0023779 | 0.203 | 0.575 | 0.0000000 |
| Rsad2 | 0e+00 | -5.7591202 | 0.070 | 0.319 | 0.0000000 |
| Trim30a | 0e+00 | -1.7869126 | 0.362 | 0.726 | 0.0000000 |
| Ifi205 | 0e+00 | -2.7641257 | 0.016 | 0.159 | 0.0000000 |
| Isg15 | 0e+00 | -4.1544408 | 0.173 | 0.460 | 0.0000000 |
| Trim30d | 0e+00 | -2.0439900 | 0.238 | 0.584 | 0.0000000 |
| Ifi213 | 0e+00 | -3.9631963 | 0.219 | 0.513 | 0.0000000 |
| Slfn2 | 0e+00 | -2.7613254 | 0.186 | 0.487 | 0.0000000 |
| Ifi47 | 0e+00 | -5.9605329 | 0.005 | 0.097 | 0.0000000 |
| Ccl2 | 0e+00 | -4.3963968 | 0.015 | 0.142 | 0.0000000 |
| Oasl1 | 0e+00 | -6.0440790 | 0.026 | 0.177 | 0.0000000 |
| Phf11d | 0e+00 | -2.6600679 | 0.158 | 0.442 | 0.0000000 |
| Ly6a | 0e+00 | -3.4065126 | 0.035 | 0.204 | 0.0000000 |
| Parp12 | 0e+00 | -1.8393088 | 0.137 | 0.416 | 0.0000000 |
| B2m | 0e+00 | -0.6968649 | 0.984 | 1.000 | 0.0000000 |
| Ifi208 | 0e+00 | -3.5788855 | 0.183 | 0.469 | 0.0000000 |
| Bst2 | 0e+00 | -1.8245625 | 0.263 | 0.558 | 0.0000000 |
| Isg20 | 0e+00 | -2.6790339 | 0.035 | 0.195 | 0.0000000 |
| Parp14 | 0e+00 | -2.5719671 | 0.257 | 0.531 | 0.0000000 |
| Herc6 | 0e+00 | -2.8622272 | 0.429 | 0.681 | 0.0000000 |
| Xaf1 | 0e+00 | -2.5040517 | 0.481 | 0.708 | 0.0000000 |
| Gbp9 | 0e+00 | -2.2293329 | 0.075 | 0.283 | 0.0000000 |
| Ddx60 | 0e+00 | -2.3006137 | 0.133 | 0.381 | 0.0000000 |
| Fcgr1 | 0e+00 | -1.1529893 | 0.634 | 0.850 | 0.0000000 |
| Tor3a | 0e+00 | -1.9524058 | 0.230 | 0.496 | 0.0000000 |
| Sp100 | 0e+00 | -2.7831339 | 0.375 | 0.611 | 0.0000000 |
| Tgtp1 | 0e+00 | -3.5557912 | 0.022 | 0.142 | 0.0000000 |
| Axl | 0e+00 | -2.0141459 | 0.106 | 0.327 | 0.0000000 |
| Etnk1 | 0e+00 | -1.3333396 | 0.288 | 0.575 | 0.0000001 |
| Gvin1 | 0e+00 | -1.9487476 | 0.297 | 0.593 | 0.0000004 |
| Slfn8 | 0e+00 | -1.9722130 | 0.439 | 0.673 | 0.0000006 |
| Irgm1 | 0e+00 | -2.4908527 | 0.340 | 0.549 | 0.0000007 |
| Ifih1 | 0e+00 | -2.2804736 | 0.163 | 0.381 | 0.0000012 |
| Ifi214 | 0e+00 | -2.5325909 | 0.216 | 0.451 | 0.0000025 |
| Ly6e | 0e+00 | -0.9653821 | 0.831 | 0.912 | 0.0000027 |
| Dhx58 | 0e+00 | -2.4560680 | 0.180 | 0.398 | 0.0000030 |
| Znfx1 | 0e+00 | -1.4570059 | 0.256 | 0.522 | 0.0000036 |
| Ctss | 0e+00 | -0.3802187 | 0.995 | 1.000 | 0.0000046 |
| Trim30c | 0e+00 | -4.9083411 | 0.013 | 0.097 | 0.0000080 |
| Slfn5 | 0e+00 | -3.0208370 | 0.527 | 0.717 | 0.0000101 |
| Parp9 | 0e+00 | -1.7350533 | 0.168 | 0.389 | 0.0000124 |
| Nampt | 0e+00 | -1.4538988 | 0.095 | 0.283 | 0.0000136 |
| Gvin3 | 0e+00 | -1.3339944 | 0.062 | 0.221 | 0.0000156 |
| Pml | 0e+00 | -1.9517895 | 0.133 | 0.336 | 0.0000183 |
| Gvin-ps7 | 0e+00 | -1.7278799 | 0.310 | 0.558 | 0.0000205 |
| Psmb8 | 0e+00 | -1.2938055 | 0.451 | 0.690 | 0.0000215 |
| H2-D1 | 0e+00 | -0.8769748 | 0.831 | 0.903 | 0.0000402 |
| Stk-ps2 | 0e+00 | -3.5651474 | 0.009 | 0.080 | 0.0000439 |
| Ifi35 | 0e+00 | -1.5238354 | 0.195 | 0.416 | 0.0000593 |
| Il18bp | 0e+00 | -4.9709430 | 0.015 | 0.097 | 0.0000633 |
| Gvin2 | 0e+00 | -1.8304393 | 0.338 | 0.593 | 0.0000734 |
| Uba7 | 0e+00 | -1.3748398 | 0.247 | 0.487 | 0.0001701 |
| Dtx3l | 0e+00 | -1.5000648 | 0.478 | 0.690 | 0.0002960 |
| Gbp2 | 0e+00 | -3.0519719 | 0.029 | 0.133 | 0.0003474 |
| Nmi | 0e+00 | -1.4919321 | 0.113 | 0.292 | 0.0004628 |
| H2-K1 | 0e+00 | -0.9577947 | 0.778 | 0.841 | 0.0004653 |
| Socs1 | 0e+00 | -2.0940465 | 0.022 | 0.115 | 0.0005418 |
| Epsti1 | 0e+00 | -1.7535665 | 0.141 | 0.336 | 0.0005803 |
| Sdc3 | 0e+00 | -1.5345282 | 0.116 | 0.292 | 0.0006269 |
| Csf1 | 1e-07 | -2.5333990 | 0.052 | 0.177 | 0.0009569 |
| Igtp | 1e-07 | -1.8254598 | 0.236 | 0.434 | 0.0010707 |
| Tcstv4 | 1e-07 | -2.7218314 | 0.028 | 0.124 | 0.0014691 |
| Ogfr | 1e-07 | -1.1826233 | 0.104 | 0.274 | 0.0015311 |
| Scimp | 1e-07 | -2.6625806 | 0.035 | 0.142 | 0.0017639 |
| P2ry12 | 3e-07 | 0.5307100 | 0.976 | 0.965 | 0.0044757 |
Microglia0_vs_Microglia5
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| H2-Ab1 | 0.0000000 | -7.4318523 | 0.049 | 0.904 | 0.0000000 |
| H2-Eb1 | 0.0000000 | -8.6687759 | 0.017 | 0.630 | 0.0000000 |
| Cd74 | 0.0000000 | -7.2094994 | 0.130 | 0.959 | 0.0000000 |
| H2-Aa | 0.0000000 | -8.4606111 | 0.103 | 0.712 | 0.0000000 |
| H2-D1 | 0.0000000 | -1.8190616 | 0.831 | 0.959 | 0.0000000 |
| H2-K1 | 0.0000000 | -1.4638914 | 0.778 | 0.932 | 0.0000000 |
| Ctss | 0.0000000 | -0.5001659 | 0.995 | 1.000 | 0.0000101 |
| H2-Oa | 0.0000000 | -1.9985115 | 0.115 | 0.356 | 0.0000127 |
| Itgax | 0.0000000 | -3.1706542 | 0.045 | 0.205 | 0.0000154 |
| Wfdc17 | 0.0000000 | -2.8723306 | 0.010 | 0.096 | 0.0000430 |
| B2m | 0.0000000 | -0.7917514 | 0.984 | 0.986 | 0.0003590 |
| H2-T11-ps | 0.0000000 | -0.7227747 | 0.105 | 0.315 | 0.0004487 |
| Pfkm | 0.0000000 | -3.0047665 | 0.008 | 0.082 | 0.0005098 |
| Cox6a2 | 0.0000000 | -2.7826451 | 0.034 | 0.164 | 0.0006196 |
| Spp1 | 0.0000001 | -7.5562557 | 0.017 | 0.110 | 0.0014588 |
| Egln3 | 0.0000001 | -2.3085412 | 0.006 | 0.068 | 0.0015874 |
| Nbl1 | 0.0000001 | -3.9810403 | 0.013 | 0.096 | 0.0022861 |
| Stab1 | 0.0000002 | 1.4428220 | 0.820 | 0.616 | 0.0032953 |
| Axl | 0.0000005 | -1.4711972 | 0.106 | 0.301 | 0.0074292 |
| Fgl2 | 0.0000006 | -1.6909638 | 0.092 | 0.274 | 0.0095163 |
| Baiap2l2 | 0.0000013 | -2.8536934 | 0.015 | 0.096 | 0.0209162 |
| Hpse | 0.0000015 | -3.9991735 | 0.012 | 0.082 | 0.0240343 |
| Usp12 | 0.0000018 | -1.5575384 | 0.200 | 0.425 | 0.0293490 |
| Tcap | 0.0000022 | -5.0279818 | 0.001 | 0.027 | 0.0351516 |
| Ly86 | 0.0000022 | -0.5983349 | 0.942 | 0.986 | 0.0352783 |
| Capg | 0.0000034 | -2.0517585 | 0.103 | 0.274 | 0.0546797 |
| Znrf3 | 0.0000037 | 0.9214717 | 0.881 | 0.753 | 0.0582910 |
| Ccl6 | 0.0000037 | -1.8924277 | 0.277 | 0.507 | 0.0591855 |
| BC106179 | 0.0000040 | 1.4987526 | 0.341 | 0.082 | 0.0643132 |
| Ccl3 | 0.0000041 | -1.3728799 | 0.093 | 0.260 | 0.0652644 |
| Mmp12 | 0.0000047 | 1.6091279 | 0.594 | 0.315 | 0.0754457 |
| H2-T23 | 0.0000071 | -1.1910011 | 0.658 | 0.808 | 0.1130697 |
| Cst7 | 0.0000112 | -2.9623410 | 0.141 | 0.301 | 0.1782549 |
| Ecscr | 0.0000118 | 1.6802238 | 0.440 | 0.178 | 0.1881133 |
| H2-Q5 | 0.0000119 | -1.9830854 | 0.143 | 0.315 | 0.1892146 |
| Tspo | 0.0000120 | -0.8627031 | 0.182 | 0.397 | 0.1909594 |
| Mtss1 | 0.0000128 | 1.4973518 | 0.691 | 0.507 | 0.2035896 |
| Nfia | 0.0000144 | 0.7716806 | 0.843 | 0.685 | 0.2300119 |
| Nox4 | 0.0000154 | 1.9389200 | 0.600 | 0.356 | 0.2451486 |
| H2-M3 | 0.0000155 | -1.3374537 | 0.208 | 0.411 | 0.2470730 |
| Atp1a3 | 0.0000158 | -1.2609123 | 0.102 | 0.260 | 0.2517892 |
| Zfp369 | 0.0000262 | 1.2163604 | 0.871 | 0.753 | 0.4179872 |
| Prr15 | 0.0000264 | 2.1017396 | 0.758 | 0.616 | 0.4215049 |
| Vmn1r76 | 0.0000265 | 1.1382475 | 0.810 | 0.562 | 0.4220682 |
| H2-Q7 | 0.0000266 | -2.5869970 | 0.468 | 0.603 | 0.4236276 |
| Rb1 | 0.0000296 | 1.3468121 | 0.505 | 0.274 | 0.4719877 |
| Psap | 0.0000325 | -0.4932126 | 0.972 | 0.986 | 0.5188936 |
| Slc25a23 | 0.0000343 | 3.0365508 | 0.309 | 0.082 | 0.5475530 |
| Ly6e | 0.0000347 | -0.8385618 | 0.831 | 0.863 | 0.5529564 |
| Ramp1 | 0.0000355 | -1.3487439 | 0.123 | 0.288 | 0.5660729 |
| Samd9l | 0.0000410 | -2.3460644 | 0.032 | 0.123 | 0.6536817 |
| Or51q1 | 0.0000415 | 1.2831293 | 0.922 | 0.795 | 0.6620993 |
| H2-Q6 | 0.0000417 | -1.6910464 | 0.295 | 0.493 | 0.6655392 |
| Dcstamp | 0.0000424 | -2.5445271 | 0.007 | 0.055 | 0.6758766 |
| Jcad | 0.0000427 | -2.4455102 | 0.007 | 0.055 | 0.6811751 |
| Serpine2 | 0.0000539 | -0.6868904 | 0.844 | 0.904 | 0.8593515 |
| Itpripl1 | 0.0000606 | 1.1461761 | 0.538 | 0.301 | 0.9664142 |
| Adora1 | 0.0000610 | -1.8310104 | 0.021 | 0.096 | 0.9729686 |
| Traf5 | 0.0000654 | 1.2367323 | 0.794 | 0.616 | 1.0000000 |
| Sh2d6 | 0.0000742 | -3.1697959 | 0.012 | 0.068 | 1.0000000 |
| Krt7 | 0.0000754 | 1.2661316 | 0.502 | 0.274 | 1.0000000 |
| Serinc3 | 0.0000852 | 0.3650067 | 0.984 | 0.986 | 1.0000000 |
| Bltp1 | 0.0000983 | 0.7262640 | 0.713 | 0.466 | 1.0000000 |
| H2-Q10 | 0.0001118 | -0.3725134 | 0.421 | 0.630 | 1.0000000 |
| Gcn1 | 0.0001227 | 1.5491535 | 0.775 | 0.630 | 1.0000000 |
| Zfp738 | 0.0001349 | 0.9844280 | 0.831 | 0.685 | 1.0000000 |
| Tsc22d1 | 0.0001463 | -3.2987462 | 0.042 | 0.137 | 1.0000000 |
| Clec7a | 0.0001509 | -1.7652091 | 0.138 | 0.288 | 1.0000000 |
| Nav2 | 0.0001628 | 0.8146888 | 0.770 | 0.616 | 1.0000000 |
| Tubb4a | 0.0001692 | -3.6385477 | 0.005 | 0.041 | 1.0000000 |
| Mrgpre | 0.0001697 | 0.1276763 | 0.467 | 0.233 | 1.0000000 |
| Crym | 0.0001767 | -3.5251688 | 0.005 | 0.041 | 1.0000000 |
| Spcs1 | 0.0001772 | -0.9868105 | 0.369 | 0.589 | 1.0000000 |
| Ctsb | 0.0001814 | -0.6662170 | 0.965 | 0.959 | 1.0000000 |
| Syngr1 | 0.0001869 | -0.8051675 | 0.676 | 0.753 | 1.0000000 |
| C1qa | 0.0001884 | -0.2906556 | 0.993 | 1.000 | 1.0000000 |
| Grk4 | 0.0001968 | 1.1218519 | 0.807 | 0.630 | 1.0000000 |
| Acnat1 | 0.0002074 | 1.1854870 | 0.758 | 0.616 | 1.0000000 |
| Dido1 | 0.0002100 | 0.7600088 | 0.846 | 0.712 | 1.0000000 |
| Pdcd1 | 0.0002302 | -1.7021805 | 0.036 | 0.123 | 1.0000000 |
| Ank3 | 0.0002332 | 1.6094905 | 0.330 | 0.123 | 1.0000000 |
| Or8b44 | 0.0002783 | 1.3357253 | 0.804 | 0.726 | 1.0000000 |
| Lpar6 | 0.0002814 | 0.9389916 | 0.690 | 0.479 | 1.0000000 |
| C1qb | 0.0003041 | -0.3651707 | 0.988 | 0.986 | 1.0000000 |
| Eef1a1 | 0.0003166 | -0.5130744 | 0.946 | 0.945 | 1.0000000 |
| Nipal2 | 0.0003181 | 1.2702075 | 0.817 | 0.712 | 1.0000000 |
| Bora | 0.0003303 | 1.4568299 | 0.504 | 0.274 | 1.0000000 |
| Klhl32 | 0.0003304 | 2.1733449 | 0.433 | 0.260 | 1.0000000 |
| Or4m1 | 0.0003624 | 1.3325952 | 0.501 | 0.288 | 1.0000000 |
| Or14j9 | 0.0003854 | -4.3027381 | 0.009 | 0.055 | 1.0000000 |
| Haus8 | 0.0003947 | 1.1059810 | 0.757 | 0.562 | 1.0000000 |
| Npc2 | 0.0003960 | -0.7483326 | 0.805 | 0.849 | 1.0000000 |
| Fbxo47 | 0.0004025 | -2.9745836 | 0.009 | 0.055 | 1.0000000 |
| Vwa3b | 0.0004033 | -3.5834292 | 0.014 | 0.068 | 1.0000000 |
| Csf1 | 0.0004128 | -1.5268798 | 0.052 | 0.151 | 1.0000000 |
| Lrrc8b | 0.0004415 | -1.6023763 | 0.009 | 0.055 | 1.0000000 |
| Vmn1r26 | 0.0004489 | 0.9660346 | 0.743 | 0.548 | 1.0000000 |
| Rps2-ps10 | 0.0004499 | 2.3088525 | 0.736 | 0.589 | 1.0000000 |
| Parva | 0.0004669 | 1.6365744 | 0.522 | 0.329 | 1.0000000 |
| Il3ra | 0.0004705 | -1.4855578 | 0.019 | 0.082 | 1.0000000 |
Microglia0_vs_Microglia5_comorbid
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| H2-Ab1 | 0.0000000 | -7.4318523 | 0.049 | 0.904 | 0.0000000 |
| H2-Eb1 | 0.0000000 | -8.6687759 | 0.017 | 0.630 | 0.0000000 |
| Cd74 | 0.0000000 | -7.2094994 | 0.130 | 0.959 | 0.0000000 |
| H2-Aa | 0.0000000 | -8.4606111 | 0.103 | 0.712 | 0.0000000 |
| H2-D1 | 0.0000000 | -1.8190616 | 0.831 | 0.959 | 0.0000000 |
| H2-K1 | 0.0000000 | -1.4638914 | 0.778 | 0.932 | 0.0000000 |
| Ctss | 0.0000000 | -0.5001659 | 0.995 | 1.000 | 0.0000101 |
| H2-Oa | 0.0000000 | -1.9985115 | 0.115 | 0.356 | 0.0000127 |
| Itgax | 0.0000000 | -3.1706542 | 0.045 | 0.205 | 0.0000154 |
| Wfdc17 | 0.0000000 | -2.8723306 | 0.010 | 0.096 | 0.0000430 |
| B2m | 0.0000000 | -0.7917514 | 0.984 | 0.986 | 0.0003590 |
| H2-T11-ps | 0.0000000 | -0.7227747 | 0.105 | 0.315 | 0.0004487 |
| Pfkm | 0.0000000 | -3.0047665 | 0.008 | 0.082 | 0.0005098 |
| Cox6a2 | 0.0000000 | -2.7826451 | 0.034 | 0.164 | 0.0006196 |
| Spp1 | 0.0000001 | -7.5562557 | 0.017 | 0.110 | 0.0014588 |
| Egln3 | 0.0000001 | -2.3085412 | 0.006 | 0.068 | 0.0015874 |
| Nbl1 | 0.0000001 | -3.9810403 | 0.013 | 0.096 | 0.0022861 |
| Stab1 | 0.0000002 | 1.4428220 | 0.820 | 0.616 | 0.0032953 |
| Axl | 0.0000005 | -1.4711972 | 0.106 | 0.301 | 0.0074292 |
| Fgl2 | 0.0000006 | -1.6909638 | 0.092 | 0.274 | 0.0095163 |
| Baiap2l2 | 0.0000013 | -2.8536934 | 0.015 | 0.096 | 0.0209162 |
| Hpse | 0.0000015 | -3.9991735 | 0.012 | 0.082 | 0.0240343 |
| Usp12 | 0.0000018 | -1.5575384 | 0.200 | 0.425 | 0.0293490 |
| Tcap | 0.0000022 | -5.0279818 | 0.001 | 0.027 | 0.0351516 |
| Ly86 | 0.0000022 | -0.5983349 | 0.942 | 0.986 | 0.0352783 |
| Capg | 0.0000034 | -2.0517585 | 0.103 | 0.274 | 0.0546797 |
| Znrf3 | 0.0000037 | 0.9214717 | 0.881 | 0.753 | 0.0582910 |
| Ccl6 | 0.0000037 | -1.8924277 | 0.277 | 0.507 | 0.0591855 |
| BC106179 | 0.0000040 | 1.4987526 | 0.341 | 0.082 | 0.0643132 |
| Ccl3 | 0.0000041 | -1.3728799 | 0.093 | 0.260 | 0.0652644 |
| Mmp12 | 0.0000047 | 1.6091279 | 0.594 | 0.315 | 0.0754457 |
| H2-T23 | 0.0000071 | -1.1910011 | 0.658 | 0.808 | 0.1130697 |
| Cst7 | 0.0000112 | -2.9623410 | 0.141 | 0.301 | 0.1782549 |
| Ecscr | 0.0000118 | 1.6802238 | 0.440 | 0.178 | 0.1881133 |
| H2-Q5 | 0.0000119 | -1.9830854 | 0.143 | 0.315 | 0.1892146 |
| Tspo | 0.0000120 | -0.8627031 | 0.182 | 0.397 | 0.1909594 |
| Mtss1 | 0.0000128 | 1.4973518 | 0.691 | 0.507 | 0.2035896 |
| Nfia | 0.0000144 | 0.7716806 | 0.843 | 0.685 | 0.2300119 |
| Nox4 | 0.0000154 | 1.9389200 | 0.600 | 0.356 | 0.2451486 |
| H2-M3 | 0.0000155 | -1.3374537 | 0.208 | 0.411 | 0.2470730 |
| Atp1a3 | 0.0000158 | -1.2609123 | 0.102 | 0.260 | 0.2517892 |
| Zfp369 | 0.0000262 | 1.2163604 | 0.871 | 0.753 | 0.4179872 |
| Prr15 | 0.0000264 | 2.1017396 | 0.758 | 0.616 | 0.4215049 |
| Vmn1r76 | 0.0000265 | 1.1382475 | 0.810 | 0.562 | 0.4220682 |
| H2-Q7 | 0.0000266 | -2.5869970 | 0.468 | 0.603 | 0.4236276 |
| Rb1 | 0.0000296 | 1.3468121 | 0.505 | 0.274 | 0.4719877 |
| Psap | 0.0000325 | -0.4932126 | 0.972 | 0.986 | 0.5188936 |
| Slc25a23 | 0.0000343 | 3.0365508 | 0.309 | 0.082 | 0.5475530 |
| Ly6e | 0.0000347 | -0.8385618 | 0.831 | 0.863 | 0.5529564 |
| Ramp1 | 0.0000355 | -1.3487439 | 0.123 | 0.288 | 0.5660729 |
| Samd9l | 0.0000410 | -2.3460644 | 0.032 | 0.123 | 0.6536817 |
| Or51q1 | 0.0000415 | 1.2831293 | 0.922 | 0.795 | 0.6620993 |
| H2-Q6 | 0.0000417 | -1.6910464 | 0.295 | 0.493 | 0.6655392 |
| Dcstamp | 0.0000424 | -2.5445271 | 0.007 | 0.055 | 0.6758766 |
| Jcad | 0.0000427 | -2.4455102 | 0.007 | 0.055 | 0.6811751 |
| Serpine2 | 0.0000539 | -0.6868904 | 0.844 | 0.904 | 0.8593515 |
| Itpripl1 | 0.0000606 | 1.1461761 | 0.538 | 0.301 | 0.9664142 |
| Adora1 | 0.0000610 | -1.8310104 | 0.021 | 0.096 | 0.9729686 |
| Traf5 | 0.0000654 | 1.2367323 | 0.794 | 0.616 | 1.0000000 |
| Sh2d6 | 0.0000742 | -3.1697959 | 0.012 | 0.068 | 1.0000000 |
| Krt7 | 0.0000754 | 1.2661316 | 0.502 | 0.274 | 1.0000000 |
| Serinc3 | 0.0000852 | 0.3650067 | 0.984 | 0.986 | 1.0000000 |
| Bltp1 | 0.0000983 | 0.7262640 | 0.713 | 0.466 | 1.0000000 |
| H2-Q10 | 0.0001118 | -0.3725134 | 0.421 | 0.630 | 1.0000000 |
| Gcn1 | 0.0001227 | 1.5491535 | 0.775 | 0.630 | 1.0000000 |
| Zfp738 | 0.0001349 | 0.9844280 | 0.831 | 0.685 | 1.0000000 |
| Tsc22d1 | 0.0001463 | -3.2987462 | 0.042 | 0.137 | 1.0000000 |
| Clec7a | 0.0001509 | -1.7652091 | 0.138 | 0.288 | 1.0000000 |
| Nav2 | 0.0001628 | 0.8146888 | 0.770 | 0.616 | 1.0000000 |
| Tubb4a | 0.0001692 | -3.6385477 | 0.005 | 0.041 | 1.0000000 |
| Mrgpre | 0.0001697 | 0.1276763 | 0.467 | 0.233 | 1.0000000 |
| Crym | 0.0001767 | -3.5251688 | 0.005 | 0.041 | 1.0000000 |
| Spcs1 | 0.0001772 | -0.9868105 | 0.369 | 0.589 | 1.0000000 |
| Ctsb | 0.0001814 | -0.6662170 | 0.965 | 0.959 | 1.0000000 |
| Syngr1 | 0.0001869 | -0.8051675 | 0.676 | 0.753 | 1.0000000 |
| C1qa | 0.0001884 | -0.2906556 | 0.993 | 1.000 | 1.0000000 |
| Grk4 | 0.0001968 | 1.1218519 | 0.807 | 0.630 | 1.0000000 |
| Acnat1 | 0.0002074 | 1.1854870 | 0.758 | 0.616 | 1.0000000 |
| Dido1 | 0.0002100 | 0.7600088 | 0.846 | 0.712 | 1.0000000 |
| Pdcd1 | 0.0002302 | -1.7021805 | 0.036 | 0.123 | 1.0000000 |
| Ank3 | 0.0002332 | 1.6094905 | 0.330 | 0.123 | 1.0000000 |
| Or8b44 | 0.0002783 | 1.3357253 | 0.804 | 0.726 | 1.0000000 |
| Lpar6 | 0.0002814 | 0.9389916 | 0.690 | 0.479 | 1.0000000 |
| C1qb | 0.0003041 | -0.3651707 | 0.988 | 0.986 | 1.0000000 |
| Eef1a1 | 0.0003166 | -0.5130744 | 0.946 | 0.945 | 1.0000000 |
| Nipal2 | 0.0003181 | 1.2702075 | 0.817 | 0.712 | 1.0000000 |
| Bora | 0.0003303 | 1.4568299 | 0.504 | 0.274 | 1.0000000 |
| Klhl32 | 0.0003304 | 2.1733449 | 0.433 | 0.260 | 1.0000000 |
| Or4m1 | 0.0003624 | 1.3325952 | 0.501 | 0.288 | 1.0000000 |
| Or14j9 | 0.0003854 | -4.3027381 | 0.009 | 0.055 | 1.0000000 |
| Haus8 | 0.0003947 | 1.1059810 | 0.757 | 0.562 | 1.0000000 |
| Npc2 | 0.0003960 | -0.7483326 | 0.805 | 0.849 | 1.0000000 |
| Fbxo47 | 0.0004025 | -2.9745836 | 0.009 | 0.055 | 1.0000000 |
| Vwa3b | 0.0004033 | -3.5834292 | 0.014 | 0.068 | 1.0000000 |
| Csf1 | 0.0004128 | -1.5268798 | 0.052 | 0.151 | 1.0000000 |
| Lrrc8b | 0.0004415 | -1.6023763 | 0.009 | 0.055 | 1.0000000 |
| Vmn1r26 | 0.0004489 | 0.9660346 | 0.743 | 0.548 | 1.0000000 |
| Rps2-ps10 | 0.0004499 | 2.3088525 | 0.736 | 0.589 | 1.0000000 |
| Parva | 0.0004669 | 1.6365744 | 0.522 | 0.329 | 1.0000000 |
| Il3ra | 0.0004705 | -1.4855578 | 0.019 | 0.082 | 1.0000000 |
Microglia1_vs_Microglia2
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Cst7 | 0 | -5.2302997 | 0.089 | 0.705 | 0 |
| Clec7a | 0 | -3.7205517 | 0.081 | 0.668 | 0 |
| Apoe | 0 | -2.6626949 | 0.578 | 0.937 | 0 |
| Lyz2 | 0 | -2.1110446 | 0.518 | 0.921 | 0 |
| Ccl3 | 0 | -4.3253455 | 0.048 | 0.533 | 0 |
| Ctsb | 0 | -1.4917025 | 0.876 | 0.993 | 0 |
| Ctsd | 0 | -1.3683941 | 0.954 | 1.000 | 0 |
| Axl | 0 | -3.1095888 | 0.073 | 0.533 | 0 |
| Ctsz | 0 | -1.3585033 | 0.837 | 0.987 | 0 |
| Cd63 | 0 | -1.6382595 | 0.511 | 0.893 | 0 |
| Lgals3bp | 0 | -2.1562683 | 0.315 | 0.758 | 0 |
| Ank | 0 | -3.9303173 | 0.066 | 0.467 | 0 |
| Ftl1 | 0 | -1.2109756 | 0.837 | 0.976 | 0 |
| Tyrobp | 0 | -1.5660059 | 0.815 | 0.980 | 0 |
| Fth1 | 0 | -1.1654732 | 0.847 | 0.983 | 0 |
| Mif | 0 | -1.7946341 | 0.149 | 0.605 | 0 |
| P2ry12 | 0 | 1.4191441 | 0.949 | 0.915 | 0 |
| B2m | 0 | -0.8797025 | 0.949 | 0.989 | 0 |
| Malat1 | 0 | 0.8542927 | 0.987 | 0.952 | 0 |
| Rps16-ps2 | 0 | -1.7881802 | 0.255 | 0.701 | 0 |
| Gnas | 0 | -1.5854706 | 0.305 | 0.734 | 0 |
| Lpl | 0 | -3.4413178 | 0.541 | 0.825 | 0 |
| Ccl4 | 0 | -6.6339512 | 0.026 | 0.332 | 0 |
| Rpl10a-ps1 | 0 | -1.9408953 | 0.133 | 0.528 | 0 |
| Hif1a | 0 | -1.7572560 | 0.170 | 0.587 | 0 |
| Ccl6 | 0 | -2.5067937 | 0.194 | 0.587 | 0 |
| Aldoa | 0 | -1.5312118 | 0.359 | 0.784 | 0 |
| Capg | 0 | -2.8656229 | 0.063 | 0.406 | 0 |
| Trac | 0 | 2.1917910 | 0.869 | 0.568 | 0 |
| Cd52 | 0 | -1.2581163 | 0.292 | 0.738 | 0 |
| Gapdh | 0 | -1.4627889 | 0.487 | 0.841 | 0 |
| Cd9 | 0 | -1.1027383 | 0.800 | 0.969 | 0 |
| Npc2 | 0 | -1.0907539 | 0.676 | 0.926 | 0 |
| Pkm | 0 | -1.5299422 | 0.242 | 0.642 | 0 |
| Lilrb4a | 0 | -3.3405404 | 0.043 | 0.345 | 0 |
| Cd74 | 0 | -2.4981197 | 0.096 | 0.443 | 0 |
| Arfgef3 | 0 | 1.5791000 | 0.874 | 0.574 | 0 |
| Cd68 | 0 | -1.0498472 | 0.690 | 0.932 | 0 |
| Ifi27l2a | 0 | -2.0662952 | 0.074 | 0.393 | 0 |
| Baiap2l2 | 0 | -5.9736114 | 0.006 | 0.238 | 0 |
| Eef1a1 | 0 | -0.7849778 | 0.884 | 0.989 | 0 |
| Ctsl | 0 | -1.0043141 | 0.796 | 0.969 | 0 |
| Myo1e | 0 | -2.6605331 | 0.059 | 0.358 | 0 |
| Anxa5 | 0 | -2.4724416 | 0.079 | 0.389 | 0 |
| Cox6a2 | 0 | -2.6062141 | 0.024 | 0.282 | 0 |
| H2-D1 | 0 | -0.9365601 | 0.706 | 0.941 | 0 |
| Syngr1 | 0 | -1.4104739 | 0.482 | 0.810 | 0 |
| Cux2 | 0 | 1.4455124 | 0.924 | 0.821 | 0 |
| Rps12l1 | 0 | -1.5296697 | 0.295 | 0.629 | 0 |
| Rps13-ps2 | 0 | -2.1192775 | 0.098 | 0.410 | 0 |
| Rps2 | 0 | -1.0391815 | 0.393 | 0.786 | 0 |
| Mt1 | 0 | -0.9889788 | 0.196 | 0.594 | 0 |
| Lipe | 0 | 1.5878442 | 0.935 | 0.830 | 0 |
| Ramp1 | 0 | -2.0524426 | 0.080 | 0.380 | 0 |
| Itgax | 0 | -2.8686871 | 0.033 | 0.286 | 0 |
| Pld3 | 0 | -1.5493614 | 0.199 | 0.557 | 0 |
| Csf1 | 0 | -2.5105916 | 0.040 | 0.301 | 0 |
| Rplp0 | 0 | -0.9805014 | 0.543 | 0.852 | 0 |
| Rps16 | 0 | -0.9344615 | 0.444 | 0.817 | 0 |
| Atp6v0c | 0 | -1.0388843 | 0.507 | 0.838 | 0 |
| Psat1 | 0 | -1.5343347 | 0.048 | 0.308 | 0 |
| Tpi1 | 0 | -1.4365039 | 0.116 | 0.441 | 0 |
| Rps5 | 0 | -1.0254345 | 0.315 | 0.679 | 0 |
| Rpl18a | 0 | -0.7951908 | 0.767 | 0.952 | 0 |
| Ucp2 | 0 | -1.4129656 | 0.210 | 0.555 | 0 |
| Pax6 | 0 | 1.6359616 | 0.846 | 0.611 | 0 |
| Tpd52 | 0 | -1.2310377 | 0.297 | 0.633 | 0 |
| Cadm1 | 0 | -1.1234179 | 0.297 | 0.651 | 0 |
| Rpl41 | 0 | -0.8072862 | 0.617 | 0.930 | 0 |
| Ch25h | 0 | -5.2138413 | 0.008 | 0.201 | 0 |
| Nceh1 | 0 | -2.4527022 | 0.068 | 0.328 | 0 |
| Cd83 | 0 | -1.2975712 | 0.279 | 0.629 | 0 |
| Igf1 | 0 | -4.3451636 | 0.101 | 0.367 | 0 |
| Rpl21 | 0 | -0.7645073 | 0.506 | 0.856 | 0 |
| Rps18 | 0 | -0.7996990 | 0.554 | 0.865 | 0 |
| Eef1b2 | 0 | -0.7655968 | 0.262 | 0.618 | 0 |
| Rpl19 | 0 | -0.8146156 | 0.399 | 0.766 | 0 |
| Rpsa | 0 | -1.0583222 | 0.293 | 0.629 | 0 |
| Gusb | 0 | -1.0060868 | 0.522 | 0.793 | 0 |
| Rbm45 | 0 | 1.6865553 | 0.841 | 0.594 | 0 |
| Vmn1r13 | 0 | 1.0814302 | 0.914 | 0.758 | 0 |
| Rpl26 | 0 | -0.7333611 | 0.437 | 0.803 | 0 |
| Uba52rt | 0 | -0.7772868 | 0.388 | 0.755 | 0 |
| Rpl29 | 0 | -0.7505988 | 0.227 | 0.561 | 0 |
| Crlf2 | 0 | -1.4283320 | 0.071 | 0.338 | 0 |
| Rpl10-ps3 | 0 | -1.2431144 | 0.409 | 0.718 | 0 |
| Rps26-ps1 | 0 | -1.6984930 | 0.135 | 0.419 | 0 |
| Hexa | 0 | -0.9791101 | 0.662 | 0.904 | 0 |
| Ndufa2 | 0 | -0.6319746 | 0.195 | 0.541 | 0 |
| Lamp1 | 0 | -0.8093437 | 0.680 | 0.915 | 0 |
| Aplp2 | 0 | -1.2985348 | 0.134 | 0.434 | 0 |
| Tmem119 | 0 | 1.2017092 | 0.872 | 0.760 | 0 |
| Lilrb4b | 0 | -1.0860176 | 0.038 | 0.264 | 0 |
| Fam20c | 0 | -3.0711934 | 0.026 | 0.227 | 0 |
| Tpt1-ps3 | 0 | -1.0787850 | 0.225 | 0.561 | 0 |
| Rpl28-ps1 | 0 | -0.3789046 | 0.159 | 0.483 | 0 |
| Rps13 | 0 | -0.5005972 | 0.295 | 0.655 | 0 |
| Serpine2 | 0 | -0.8796995 | 0.701 | 0.928 | 0 |
| Galntl6 | 0 | 1.8506210 | 0.867 | 0.609 | 0 |
| Rps25 | 0 | -0.5945093 | 0.615 | 0.865 | 0 |
Microglia1_vs_Microglia2_comorbid
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Cst7 | 0 | -5.2302997 | 0.089 | 0.705 | 0 |
| Clec7a | 0 | -3.7205517 | 0.081 | 0.668 | 0 |
| Apoe | 0 | -2.6626949 | 0.578 | 0.937 | 0 |
| Lyz2 | 0 | -2.1110446 | 0.518 | 0.921 | 0 |
| Ccl3 | 0 | -4.3253455 | 0.048 | 0.533 | 0 |
| Ctsb | 0 | -1.4917025 | 0.876 | 0.993 | 0 |
| Ctsd | 0 | -1.3683941 | 0.954 | 1.000 | 0 |
| Axl | 0 | -3.1095888 | 0.073 | 0.533 | 0 |
| Ctsz | 0 | -1.3585033 | 0.837 | 0.987 | 0 |
| Cd63 | 0 | -1.6382595 | 0.511 | 0.893 | 0 |
| Lgals3bp | 0 | -2.1562683 | 0.315 | 0.758 | 0 |
| Ank | 0 | -3.9303173 | 0.066 | 0.467 | 0 |
| Ftl1 | 0 | -1.2109756 | 0.837 | 0.976 | 0 |
| Tyrobp | 0 | -1.5660059 | 0.815 | 0.980 | 0 |
| Fth1 | 0 | -1.1654732 | 0.847 | 0.983 | 0 |
| Mif | 0 | -1.7946341 | 0.149 | 0.605 | 0 |
| P2ry12 | 0 | 1.4191441 | 0.949 | 0.915 | 0 |
| B2m | 0 | -0.8797025 | 0.949 | 0.989 | 0 |
| Malat1 | 0 | 0.8542927 | 0.987 | 0.952 | 0 |
| Rps16-ps2 | 0 | -1.7881802 | 0.255 | 0.701 | 0 |
| Gnas | 0 | -1.5854706 | 0.305 | 0.734 | 0 |
| Lpl | 0 | -3.4413178 | 0.541 | 0.825 | 0 |
| Ccl4 | 0 | -6.6339512 | 0.026 | 0.332 | 0 |
| Rpl10a-ps1 | 0 | -1.9408953 | 0.133 | 0.528 | 0 |
| Hif1a | 0 | -1.7572560 | 0.170 | 0.587 | 0 |
| Ccl6 | 0 | -2.5067937 | 0.194 | 0.587 | 0 |
| Aldoa | 0 | -1.5312118 | 0.359 | 0.784 | 0 |
| Capg | 0 | -2.8656229 | 0.063 | 0.406 | 0 |
| Trac | 0 | 2.1917910 | 0.869 | 0.568 | 0 |
| Cd52 | 0 | -1.2581163 | 0.292 | 0.738 | 0 |
| Gapdh | 0 | -1.4627889 | 0.487 | 0.841 | 0 |
| Cd9 | 0 | -1.1027383 | 0.800 | 0.969 | 0 |
| Npc2 | 0 | -1.0907539 | 0.676 | 0.926 | 0 |
| Pkm | 0 | -1.5299422 | 0.242 | 0.642 | 0 |
| Lilrb4a | 0 | -3.3405404 | 0.043 | 0.345 | 0 |
| Cd74 | 0 | -2.4981197 | 0.096 | 0.443 | 0 |
| Arfgef3 | 0 | 1.5791000 | 0.874 | 0.574 | 0 |
| Cd68 | 0 | -1.0498472 | 0.690 | 0.932 | 0 |
| Ifi27l2a | 0 | -2.0662952 | 0.074 | 0.393 | 0 |
| Baiap2l2 | 0 | -5.9736114 | 0.006 | 0.238 | 0 |
| Eef1a1 | 0 | -0.7849778 | 0.884 | 0.989 | 0 |
| Ctsl | 0 | -1.0043141 | 0.796 | 0.969 | 0 |
| Myo1e | 0 | -2.6605331 | 0.059 | 0.358 | 0 |
| Anxa5 | 0 | -2.4724416 | 0.079 | 0.389 | 0 |
| Cox6a2 | 0 | -2.6062141 | 0.024 | 0.282 | 0 |
| H2-D1 | 0 | -0.9365601 | 0.706 | 0.941 | 0 |
| Syngr1 | 0 | -1.4104739 | 0.482 | 0.810 | 0 |
| Cux2 | 0 | 1.4455124 | 0.924 | 0.821 | 0 |
| Rps12l1 | 0 | -1.5296697 | 0.295 | 0.629 | 0 |
| Rps13-ps2 | 0 | -2.1192775 | 0.098 | 0.410 | 0 |
| Rps2 | 0 | -1.0391815 | 0.393 | 0.786 | 0 |
| Mt1 | 0 | -0.9889788 | 0.196 | 0.594 | 0 |
| Lipe | 0 | 1.5878442 | 0.935 | 0.830 | 0 |
| Ramp1 | 0 | -2.0524426 | 0.080 | 0.380 | 0 |
| Itgax | 0 | -2.8686871 | 0.033 | 0.286 | 0 |
| Pld3 | 0 | -1.5493614 | 0.199 | 0.557 | 0 |
| Csf1 | 0 | -2.5105916 | 0.040 | 0.301 | 0 |
| Rplp0 | 0 | -0.9805014 | 0.543 | 0.852 | 0 |
| Rps16 | 0 | -0.9344615 | 0.444 | 0.817 | 0 |
| Atp6v0c | 0 | -1.0388843 | 0.507 | 0.838 | 0 |
| Psat1 | 0 | -1.5343347 | 0.048 | 0.308 | 0 |
| Tpi1 | 0 | -1.4365039 | 0.116 | 0.441 | 0 |
| Rps5 | 0 | -1.0254345 | 0.315 | 0.679 | 0 |
| Rpl18a | 0 | -0.7951908 | 0.767 | 0.952 | 0 |
| Ucp2 | 0 | -1.4129656 | 0.210 | 0.555 | 0 |
| Pax6 | 0 | 1.6359616 | 0.846 | 0.611 | 0 |
| Tpd52 | 0 | -1.2310377 | 0.297 | 0.633 | 0 |
| Cadm1 | 0 | -1.1234179 | 0.297 | 0.651 | 0 |
| Rpl41 | 0 | -0.8072862 | 0.617 | 0.930 | 0 |
| Ch25h | 0 | -5.2138413 | 0.008 | 0.201 | 0 |
| Nceh1 | 0 | -2.4527022 | 0.068 | 0.328 | 0 |
| Cd83 | 0 | -1.2975712 | 0.279 | 0.629 | 0 |
| Igf1 | 0 | -4.3451636 | 0.101 | 0.367 | 0 |
| Rpl21 | 0 | -0.7645073 | 0.506 | 0.856 | 0 |
| Rps18 | 0 | -0.7996990 | 0.554 | 0.865 | 0 |
| Eef1b2 | 0 | -0.7655968 | 0.262 | 0.618 | 0 |
| Rpl19 | 0 | -0.8146156 | 0.399 | 0.766 | 0 |
| Rpsa | 0 | -1.0583222 | 0.293 | 0.629 | 0 |
| Gusb | 0 | -1.0060868 | 0.522 | 0.793 | 0 |
| Rbm45 | 0 | 1.6865553 | 0.841 | 0.594 | 0 |
| Vmn1r13 | 0 | 1.0814302 | 0.914 | 0.758 | 0 |
| Rpl26 | 0 | -0.7333611 | 0.437 | 0.803 | 0 |
| Uba52rt | 0 | -0.7772868 | 0.388 | 0.755 | 0 |
| Rpl29 | 0 | -0.7505988 | 0.227 | 0.561 | 0 |
| Crlf2 | 0 | -1.4283320 | 0.071 | 0.338 | 0 |
| Rpl10-ps3 | 0 | -1.2431144 | 0.409 | 0.718 | 0 |
| Rps26-ps1 | 0 | -1.6984930 | 0.135 | 0.419 | 0 |
| Hexa | 0 | -0.9791101 | 0.662 | 0.904 | 0 |
| Ndufa2 | 0 | -0.6319746 | 0.195 | 0.541 | 0 |
| Lamp1 | 0 | -0.8093437 | 0.680 | 0.915 | 0 |
| Aplp2 | 0 | -1.2985348 | 0.134 | 0.434 | 0 |
| Tmem119 | 0 | 1.2017092 | 0.872 | 0.760 | 0 |
| Lilrb4b | 0 | -1.0860176 | 0.038 | 0.264 | 0 |
| Fam20c | 0 | -3.0711934 | 0.026 | 0.227 | 0 |
| Tpt1-ps3 | 0 | -1.0787850 | 0.225 | 0.561 | 0 |
| Rpl28-ps1 | 0 | -0.3789046 | 0.159 | 0.483 | 0 |
| Rps13 | 0 | -0.5005972 | 0.295 | 0.655 | 0 |
| Serpine2 | 0 | -0.8796995 | 0.701 | 0.928 | 0 |
| Galntl6 | 0 | 1.8506210 | 0.867 | 0.609 | 0 |
| Rps25 | 0 | -0.5945093 | 0.615 | 0.865 | 0 |
Microglia1_vs_Microglia3
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-32.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| C1qc | 0 | 1.0213634 | 0.959 | 0.729 | 0 |
| C1qa | 0 | 0.9620201 | 0.944 | 0.675 | 0 |
| Csf1r | 0 | 0.9534023 | 0.956 | 0.759 | 0 |
| Ctsd | 0 | 0.9241694 | 0.954 | 0.793 | 0 |
| Laptm5 | 0 | 0.9943457 | 0.917 | 0.665 | 0 |
| Olfml3 | 0 | 1.2178115 | 0.875 | 0.586 | 0 |
| Rab3gap1 | 0 | 2.4087082 | 0.636 | 0.207 | 0 |
| Ubb | 0 | 0.8321054 | 0.824 | 0.394 | 0 |
| Serinc3 | 0 | 0.6360570 | 0.946 | 0.714 | 0 |
| Psap | 0 | 0.8041872 | 0.894 | 0.626 | 0 |
| Lgmn | 0 | 0.7549278 | 0.961 | 0.788 | 0 |
| Or8b44 | 0 | -4.3679983 | 0.896 | 0.921 | 0 |
| Tmem119 | 0 | 0.9274532 | 0.872 | 0.576 | 0 |
| Ppp2r5a | 0 | 1.2131561 | 0.586 | 0.182 | 0 |
| H2-D1 | 0 | 1.5052900 | 0.706 | 0.355 | 0 |
| Selplg | 0 | 0.7499584 | 0.924 | 0.670 | 0 |
| Selenop | 0 | 0.6341759 | 0.852 | 0.512 | 0 |
| Serpine2 | 0 | 1.6932107 | 0.701 | 0.369 | 0 |
| Man2b1 | 0 | 0.8586168 | 0.742 | 0.399 | 0 |
| Rps27 | 0 | 0.5457671 | 0.791 | 0.360 | 0 |
| Vmn1r13 | 0 | -3.8768569 | 0.914 | 0.946 | 0 |
| Ctss | 0 | 0.6319094 | 0.987 | 0.847 | 0 |
| Bmp2k | 0 | 0.6160680 | 0.831 | 0.468 | 0 |
| Lpcat2 | 0 | 0.6024650 | 0.809 | 0.463 | 0 |
| Pdia3 | 0 | 1.0990126 | 0.675 | 0.325 | 0 |
| Trem2 | 0 | 0.8274776 | 0.841 | 0.527 | 0 |
| Rsrp1 | 0 | 0.8015566 | 0.800 | 0.468 | 0 |
| Ctsb | 0 | 0.6224608 | 0.876 | 0.586 | 0 |
| Cep85 | 0 | 1.0971267 | 0.746 | 0.360 | 0 |
| Cd81 | 0 | 0.7046374 | 0.926 | 0.724 | 0 |
| Fth1 | 0 | 0.5023903 | 0.847 | 0.581 | 0 |
| Ly86 | 0 | 0.4876841 | 0.847 | 0.512 | 0 |
| Cx3cr1 | 0 | 0.6926145 | 0.945 | 0.704 | 0 |
| Ctsz | 0 | 0.6867657 | 0.837 | 0.552 | 0 |
| Dbf4 | 0 | 2.0923392 | 0.454 | 0.108 | 0 |
| Son | 0 | 0.3988073 | 0.862 | 0.522 | 0 |
| Tgfbr1 | 0 | 0.3728372 | 0.886 | 0.571 | 0 |
| Noct | 0 | 0.5270758 | 0.778 | 0.409 | 0 |
| Fcgr3 | 0 | 0.3950869 | 0.867 | 0.567 | 0 |
| Slc38a6 | 0 | 0.5948235 | 0.718 | 0.369 | 0 |
| Pikfyve | 0 | 0.1622974 | 0.700 | 0.296 | 0 |
| Tmem234 | 0 | 2.7136153 | 0.569 | 0.212 | 0 |
| Cd9 | 0 | 0.9451968 | 0.800 | 0.537 | 0 |
| C1qb | 0 | 0.6719789 | 0.949 | 0.749 | 0 |
| Fyco1 | 0 | 1.4604339 | 0.537 | 0.182 | 0 |
| Ifngr1 | 0 | 0.2276859 | 0.801 | 0.473 | 0 |
| Dleu2 | 0 | 0.6787359 | 0.710 | 0.335 | 0 |
| Chd9 | 0 | 0.1334925 | 0.807 | 0.433 | 0 |
| Rnaset2a | 0 | 1.3095067 | 0.668 | 0.325 | 0 |
| Rpl18a | 0 | 0.3416075 | 0.767 | 0.389 | 0 |
| Ctsh | 0 | 0.0247743 | 0.675 | 0.379 | 0 |
| Ftl1 | 0 | 0.5053478 | 0.837 | 0.517 | 0 |
| Rhoa | 0 | 0.8140671 | 0.661 | 0.315 | 0 |
| Frmd4a | 0 | 0.6215722 | 0.636 | 0.286 | 0 |
| Jund | 0 | 0.4692998 | 0.527 | 0.187 | 0 |
| Hsp90b1 | 0 | 0.4945921 | 0.662 | 0.330 | 0 |
| Ubc | 0 | 1.5295952 | 0.643 | 0.330 | 0 |
| Srrm2 | 0 | 0.3832654 | 0.822 | 0.483 | 0 |
| Eif2a | 0 | -2.9569058 | 0.937 | 0.941 | 0 |
| Tprkb | 0 | -0.7201418 | 0.463 | 0.133 | 0 |
| Lman2l | 0 | 0.3461597 | 0.635 | 0.286 | 0 |
| Ctsa | 0 | 0.5659041 | 0.788 | 0.502 | 0 |
| Dnajb14 | 0 | 1.6227726 | 0.514 | 0.177 | 0 |
| Lair1 | 0 | 1.0255420 | 0.717 | 0.429 | 0 |
| Trf | 0 | 0.2244779 | 0.786 | 0.488 | 0 |
| Sirt5 | 0 | 1.0384590 | 0.672 | 0.330 | 0 |
| Arhgef40 | 0 | 0.5835365 | 0.612 | 0.251 | 0 |
| Bin1 | 0 | 0.5626523 | 0.574 | 0.227 | 0 |
| Inpp5d | 0 | 0.4020445 | 0.690 | 0.355 | 0 |
| Sfi1 | 0 | 1.6708805 | 0.617 | 0.291 | 0 |
| Upf3a | 0 | 2.0410249 | 0.537 | 0.187 | 0 |
| Unc93b1 | 0 | 0.6611136 | 0.692 | 0.365 | 0 |
| Nisch | 0 | 1.6147044 | 0.675 | 0.335 | 0 |
| Rigi | 0 | 3.9273355 | 0.496 | 0.177 | 0 |
| Cyth4 | 0 | 1.1341181 | 0.696 | 0.389 | 0 |
| Agl | 0 | 2.6402833 | 0.487 | 0.163 | 0 |
| Pld4 | 0 | 1.0602185 | 0.756 | 0.498 | 0 |
| Vps13d | 0 | 2.1403831 | 0.559 | 0.217 | 0 |
| Actb | 0 | 0.4233667 | 0.987 | 0.921 | 0 |
| Scamp2 | 0 | 0.7599338 | 0.588 | 0.296 | 0 |
| Tmcc3 | 0 | 1.6289870 | 0.428 | 0.118 | 0 |
| Trmt1l | 0 | 0.2015740 | 0.613 | 0.236 | 0 |
| Hexb | 0 | 0.5360910 | 0.992 | 0.882 | 0 |
| mt-Co1 | 0 | 0.3127764 | 0.870 | 0.567 | 0 |
| Hspa8 | 0 | 0.9055108 | 0.686 | 0.374 | 0 |
| Plxdc2 | 0 | 1.4892885 | 0.656 | 0.384 | 0 |
| Tmbim6 | 0 | 1.2221333 | 0.667 | 0.365 | 0 |
| Qki | 0 | 0.7493048 | 0.796 | 0.453 | 0 |
| Nrros | 0 | 0.3626514 | 0.594 | 0.261 | 0 |
| Elmo1 | 0 | 1.5622476 | 0.592 | 0.286 | 0 |
| H3f3b | 0 | 0.3823258 | 0.725 | 0.365 | 0 |
| Tcf7l2 | 0 | -3.5281143 | 0.884 | 0.921 | 0 |
| Cdc40 | 0 | 2.6836665 | 0.433 | 0.133 | 0 |
| Ubb-ps | 0 | 0.3791072 | 0.795 | 0.399 | 0 |
| Pag1 | 0 | 1.8918038 | 0.503 | 0.192 | 0 |
| Sft2d1 | 0 | 0.5196270 | 0.642 | 0.320 | 0 |
| Rbm39 | 0 | 0.4898347 | 0.753 | 0.424 | 0 |
| Cd80 | 0 | 2.4457863 | 0.424 | 0.118 | 0 |
| Siglech | 0 | 0.5576991 | 0.882 | 0.616 | 0 |
| Mpeg1 | 0 | 0.5858987 | 0.726 | 0.404 | 0 |
Microglia1_vs_Microglia3_comorbid
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-35.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| C1qc | 0 | 1.0213634 | 0.959 | 0.729 | 0 |
| C1qa | 0 | 0.9620201 | 0.944 | 0.675 | 0 |
| Csf1r | 0 | 0.9534023 | 0.956 | 0.759 | 0 |
| Ctsd | 0 | 0.9241694 | 0.954 | 0.793 | 0 |
| Laptm5 | 0 | 0.9943457 | 0.917 | 0.665 | 0 |
| Olfml3 | 0 | 1.2178115 | 0.875 | 0.586 | 0 |
| Rab3gap1 | 0 | 2.4087082 | 0.636 | 0.207 | 0 |
| Ubb | 0 | 0.8321054 | 0.824 | 0.394 | 0 |
| Serinc3 | 0 | 0.6360570 | 0.946 | 0.714 | 0 |
| Psap | 0 | 0.8041872 | 0.894 | 0.626 | 0 |
| Lgmn | 0 | 0.7549278 | 0.961 | 0.788 | 0 |
| Or8b44 | 0 | -4.3679983 | 0.896 | 0.921 | 0 |
| Tmem119 | 0 | 0.9274532 | 0.872 | 0.576 | 0 |
| Ppp2r5a | 0 | 1.2131561 | 0.586 | 0.182 | 0 |
| H2-D1 | 0 | 1.5052900 | 0.706 | 0.355 | 0 |
| Selplg | 0 | 0.7499584 | 0.924 | 0.670 | 0 |
| Selenop | 0 | 0.6341759 | 0.852 | 0.512 | 0 |
| Serpine2 | 0 | 1.6932107 | 0.701 | 0.369 | 0 |
| Man2b1 | 0 | 0.8586168 | 0.742 | 0.399 | 0 |
| Rps27 | 0 | 0.5457671 | 0.791 | 0.360 | 0 |
| Vmn1r13 | 0 | -3.8768569 | 0.914 | 0.946 | 0 |
| Ctss | 0 | 0.6319094 | 0.987 | 0.847 | 0 |
| Bmp2k | 0 | 0.6160680 | 0.831 | 0.468 | 0 |
| Lpcat2 | 0 | 0.6024650 | 0.809 | 0.463 | 0 |
| Pdia3 | 0 | 1.0990126 | 0.675 | 0.325 | 0 |
| Trem2 | 0 | 0.8274776 | 0.841 | 0.527 | 0 |
| Rsrp1 | 0 | 0.8015566 | 0.800 | 0.468 | 0 |
| Ctsb | 0 | 0.6224608 | 0.876 | 0.586 | 0 |
| Cep85 | 0 | 1.0971267 | 0.746 | 0.360 | 0 |
| Cd81 | 0 | 0.7046374 | 0.926 | 0.724 | 0 |
| Fth1 | 0 | 0.5023903 | 0.847 | 0.581 | 0 |
| Ly86 | 0 | 0.4876841 | 0.847 | 0.512 | 0 |
| Cx3cr1 | 0 | 0.6926145 | 0.945 | 0.704 | 0 |
| Ctsz | 0 | 0.6867657 | 0.837 | 0.552 | 0 |
| Dbf4 | 0 | 2.0923392 | 0.454 | 0.108 | 0 |
| Son | 0 | 0.3988073 | 0.862 | 0.522 | 0 |
| Tgfbr1 | 0 | 0.3728372 | 0.886 | 0.571 | 0 |
| Noct | 0 | 0.5270758 | 0.778 | 0.409 | 0 |
| Fcgr3 | 0 | 0.3950869 | 0.867 | 0.567 | 0 |
| Slc38a6 | 0 | 0.5948235 | 0.718 | 0.369 | 0 |
| Pikfyve | 0 | 0.1622974 | 0.700 | 0.296 | 0 |
| Tmem234 | 0 | 2.7136153 | 0.569 | 0.212 | 0 |
| Cd9 | 0 | 0.9451968 | 0.800 | 0.537 | 0 |
| C1qb | 0 | 0.6719789 | 0.949 | 0.749 | 0 |
| Fyco1 | 0 | 1.4604339 | 0.537 | 0.182 | 0 |
| Ifngr1 | 0 | 0.2276859 | 0.801 | 0.473 | 0 |
| Dleu2 | 0 | 0.6787359 | 0.710 | 0.335 | 0 |
| Chd9 | 0 | 0.1334925 | 0.807 | 0.433 | 0 |
| Rnaset2a | 0 | 1.3095067 | 0.668 | 0.325 | 0 |
| Rpl18a | 0 | 0.3416075 | 0.767 | 0.389 | 0 |
| Ctsh | 0 | 0.0247743 | 0.675 | 0.379 | 0 |
| Ftl1 | 0 | 0.5053478 | 0.837 | 0.517 | 0 |
| Rhoa | 0 | 0.8140671 | 0.661 | 0.315 | 0 |
| Frmd4a | 0 | 0.6215722 | 0.636 | 0.286 | 0 |
| Jund | 0 | 0.4692998 | 0.527 | 0.187 | 0 |
| Hsp90b1 | 0 | 0.4945921 | 0.662 | 0.330 | 0 |
| Ubc | 0 | 1.5295952 | 0.643 | 0.330 | 0 |
| Srrm2 | 0 | 0.3832654 | 0.822 | 0.483 | 0 |
| Eif2a | 0 | -2.9569058 | 0.937 | 0.941 | 0 |
| Tprkb | 0 | -0.7201418 | 0.463 | 0.133 | 0 |
| Lman2l | 0 | 0.3461597 | 0.635 | 0.286 | 0 |
| Ctsa | 0 | 0.5659041 | 0.788 | 0.502 | 0 |
| Dnajb14 | 0 | 1.6227726 | 0.514 | 0.177 | 0 |
| Lair1 | 0 | 1.0255420 | 0.717 | 0.429 | 0 |
| Trf | 0 | 0.2244779 | 0.786 | 0.488 | 0 |
| Sirt5 | 0 | 1.0384590 | 0.672 | 0.330 | 0 |
| Arhgef40 | 0 | 0.5835365 | 0.612 | 0.251 | 0 |
| Bin1 | 0 | 0.5626523 | 0.574 | 0.227 | 0 |
| Inpp5d | 0 | 0.4020445 | 0.690 | 0.355 | 0 |
| Sfi1 | 0 | 1.6708805 | 0.617 | 0.291 | 0 |
| Upf3a | 0 | 2.0410249 | 0.537 | 0.187 | 0 |
| Unc93b1 | 0 | 0.6611136 | 0.692 | 0.365 | 0 |
| Nisch | 0 | 1.6147044 | 0.675 | 0.335 | 0 |
| Rigi | 0 | 3.9273355 | 0.496 | 0.177 | 0 |
| Cyth4 | 0 | 1.1341181 | 0.696 | 0.389 | 0 |
| Agl | 0 | 2.6402833 | 0.487 | 0.163 | 0 |
| Pld4 | 0 | 1.0602185 | 0.756 | 0.498 | 0 |
| Vps13d | 0 | 2.1403831 | 0.559 | 0.217 | 0 |
| Actb | 0 | 0.4233667 | 0.987 | 0.921 | 0 |
| Scamp2 | 0 | 0.7599338 | 0.588 | 0.296 | 0 |
| Tmcc3 | 0 | 1.6289870 | 0.428 | 0.118 | 0 |
| Trmt1l | 0 | 0.2015740 | 0.613 | 0.236 | 0 |
| Hexb | 0 | 0.5360910 | 0.992 | 0.882 | 0 |
| mt-Co1 | 0 | 0.3127764 | 0.870 | 0.567 | 0 |
| Hspa8 | 0 | 0.9055108 | 0.686 | 0.374 | 0 |
| Plxdc2 | 0 | 1.4892885 | 0.656 | 0.384 | 0 |
| Tmbim6 | 0 | 1.2221333 | 0.667 | 0.365 | 0 |
| Qki | 0 | 0.7493048 | 0.796 | 0.453 | 0 |
| Nrros | 0 | 0.3626514 | 0.594 | 0.261 | 0 |
| Elmo1 | 0 | 1.5622476 | 0.592 | 0.286 | 0 |
| H3f3b | 0 | 0.3823258 | 0.725 | 0.365 | 0 |
| Tcf7l2 | 0 | -3.5281143 | 0.884 | 0.921 | 0 |
| Cdc40 | 0 | 2.6836665 | 0.433 | 0.133 | 0 |
| Ubb-ps | 0 | 0.3791072 | 0.795 | 0.399 | 0 |
| Pag1 | 0 | 1.8918038 | 0.503 | 0.192 | 0 |
| Sft2d1 | 0 | 0.5196270 | 0.642 | 0.320 | 0 |
| Rbm39 | 0 | 0.4898347 | 0.753 | 0.424 | 0 |
| Cd80 | 0 | 2.4457863 | 0.424 | 0.118 | 0 |
| Siglech | 0 | 0.5576991 | 0.882 | 0.616 | 0 |
| Mpeg1 | 0 | 0.5858987 | 0.726 | 0.404 | 0 |
Microglia1_vs_Microglia4
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Ifit3 | 0 | -7.6836575 | 0.035 | 0.628 | 0e+00 |
| Rtp4 | 0 | -3.4269783 | 0.093 | 0.717 | 0e+00 |
| Ifit2 | 0 | -5.7226144 | 0.020 | 0.425 | 0e+00 |
| Ifi206 | 0 | -5.9016986 | 0.005 | 0.319 | 0e+00 |
| Irf7 | 0 | -5.2595288 | 0.020 | 0.398 | 0e+00 |
| Oas2 | 0 | -6.9393210 | 0.009 | 0.327 | 0e+00 |
| Ccl12 | 0 | -4.0601690 | 0.134 | 0.690 | 0e+00 |
| Ifitm3 | 0 | -4.0940045 | 0.078 | 0.566 | 0e+00 |
| Oas1a | 0 | -3.7958610 | 0.039 | 0.460 | 0e+00 |
| Oasl2 | 0 | -6.6386633 | 0.151 | 0.673 | 0e+00 |
| Mx1 | 0 | -5.7190001 | 0.071 | 0.522 | 0e+00 |
| Usp18 | 0 | -4.2357222 | 0.060 | 0.504 | 0e+00 |
| Stat1 | 0 | -2.9876200 | 0.255 | 0.823 | 0e+00 |
| Ifi27l2a | 0 | -3.2639683 | 0.074 | 0.540 | 0e+00 |
| Tgtp2 | 0 | -5.9720180 | 0.034 | 0.389 | 0e+00 |
| Ifi211 | 0 | -6.0183554 | 0.009 | 0.283 | 0e+00 |
| Ifi207 | 0 | -5.7326783 | 0.025 | 0.354 | 0e+00 |
| Ifit3b | 0 | -8.0293608 | 0.081 | 0.504 | 0e+00 |
| Oas1g | 0 | -3.4631047 | 0.039 | 0.407 | 0e+00 |
| Nlrc5 | 0 | -2.8635630 | 0.045 | 0.425 | 0e+00 |
| Mx2 | 0 | -4.5855953 | 0.019 | 0.310 | 0e+00 |
| Zbp1 | 0 | -4.9466230 | 0.035 | 0.363 | 0e+00 |
| Lgals3bp | 0 | -2.5751171 | 0.315 | 0.814 | 0e+00 |
| Rnf213 | 0 | -2.5193816 | 0.139 | 0.628 | 0e+00 |
| Phf11b | 0 | -3.8510101 | 0.045 | 0.389 | 0e+00 |
| Trim30a | 0 | -1.9922470 | 0.230 | 0.726 | 0e+00 |
| Ifi209 | 0 | -3.6612821 | 0.088 | 0.469 | 0e+00 |
| Trex1 | 0 | -2.3489345 | 0.128 | 0.575 | 0e+00 |
| Phf11a | 0 | -5.1883581 | 0.039 | 0.345 | 0e+00 |
| Iigp1 | 0 | -5.3856932 | 0.141 | 0.558 | 0e+00 |
| Ifit1 | 0 | -6.5414183 | 0.051 | 0.363 | 0e+00 |
| Iigp1c | 0 | -3.4666543 | 0.189 | 0.602 | 0e+00 |
| Fgl2 | 0 | -2.9387304 | 0.076 | 0.442 | 0e+00 |
| Trim30d | 0 | -2.1350605 | 0.148 | 0.584 | 0e+00 |
| Ifi204 | 0 | -2.9241664 | 0.307 | 0.726 | 0e+00 |
| Helz2 | 0 | -9.1157491 | 0.008 | 0.195 | 0e+00 |
| Parp12 | 0 | -2.4273847 | 0.075 | 0.416 | 0e+00 |
| Rsad2 | 0 | -6.8488297 | 0.044 | 0.319 | 0e+00 |
| Gvin1 | 0 | -2.1665846 | 0.161 | 0.593 | 0e+00 |
| Cmpk2 | 0 | -5.1802465 | 0.004 | 0.159 | 0e+00 |
| Tor3a | 0 | -1.4478519 | 0.121 | 0.496 | 0e+00 |
| Ifi213 | 0 | -5.6531206 | 0.156 | 0.513 | 0e+00 |
| Slfn2 | 0 | -3.1617971 | 0.128 | 0.487 | 0e+00 |
| Bst2 | 0 | -2.0339628 | 0.166 | 0.558 | 0e+00 |
| Gvin2 | 0 | -2.3457184 | 0.180 | 0.593 | 0e+00 |
| Oasl1 | 0 | -8.3848299 | 0.010 | 0.177 | 0e+00 |
| Samd9l | 0 | -2.3838732 | 0.030 | 0.257 | 0e+00 |
| Isg15 | 0 | -3.6217003 | 0.133 | 0.460 | 0e+00 |
| Phf11d | 0 | -2.8198216 | 0.114 | 0.442 | 0e+00 |
| Ifi208 | 0 | -3.6570245 | 0.130 | 0.469 | 0e+00 |
| Slfn8 | 0 | -1.8602422 | 0.267 | 0.673 | 0e+00 |
| Parp9 | 0 | -2.2835738 | 0.085 | 0.389 | 0e+00 |
| Ifi214 | 0 | -3.2801761 | 0.123 | 0.451 | 0e+00 |
| Parp14 | 0 | -2.7384079 | 0.196 | 0.531 | 0e+00 |
| Ifi205 | 0 | -4.1872323 | 0.010 | 0.159 | 0e+00 |
| Sp100 | 0 | -2.8012144 | 0.287 | 0.611 | 0e+00 |
| Herc6 | 0 | -2.6516256 | 0.358 | 0.681 | 0e+00 |
| Gvin-ps7 | 0 | -2.2710598 | 0.207 | 0.558 | 0e+00 |
| Xaf1 | 0 | -2.4885923 | 0.406 | 0.708 | 0e+00 |
| Psmb8 | 0 | -1.4728430 | 0.308 | 0.690 | 0e+00 |
| Ly6a | 0 | -2.7870305 | 0.024 | 0.204 | 0e+00 |
| Etnk1 | 0 | -1.5101625 | 0.218 | 0.575 | 0e+00 |
| Fcgr1 | 0 | -1.1017639 | 0.477 | 0.850 | 0e+00 |
| Axl | 0 | -2.5188740 | 0.073 | 0.327 | 0e+00 |
| Irgm1 | 0 | -2.5222329 | 0.234 | 0.549 | 0e+00 |
| Ifih1 | 0 | -1.8123811 | 0.103 | 0.381 | 0e+00 |
| Nampt | 0 | -2.3772952 | 0.056 | 0.283 | 0e+00 |
| Ly6e | 0 | -1.2520987 | 0.680 | 0.912 | 0e+00 |
| Ifi35 | 0 | -1.5997760 | 0.116 | 0.416 | 0e+00 |
| Gbp9 | 0 | -1.4750605 | 0.056 | 0.283 | 0e+00 |
| Slfn5 | 0 | -2.1892455 | 0.421 | 0.717 | 0e+00 |
| Znfx1 | 0 | -1.6048796 | 0.194 | 0.522 | 0e+00 |
| Ddx60 | 0 | -1.8121202 | 0.109 | 0.381 | 0e+00 |
| B2m | 0 | -0.6923878 | 0.949 | 1.000 | 0e+00 |
| Isg20 | 0 | -1.5801535 | 0.028 | 0.195 | 0e+00 |
| Dhx58 | 0 | -3.0240630 | 0.134 | 0.398 | 0e+00 |
| Dtx3l | 0 | -1.5922911 | 0.363 | 0.690 | 0e+00 |
| Sdc3 | 0 | -2.3546565 | 0.069 | 0.292 | 0e+00 |
| Ifi47 | 0 | -6.8057973 | 0.004 | 0.097 | 0e+00 |
| Epsti1 | 0 | -1.6691286 | 0.089 | 0.336 | 0e+00 |
| Eif2ak2 | 0 | -1.1031130 | 0.494 | 0.779 | 0e+00 |
| Trafd1 | 0 | -1.5215331 | 0.190 | 0.496 | 0e+00 |
| Trem6l | 0 | -2.3008212 | 0.099 | 0.336 | 0e+00 |
| Tap1 | 0 | -1.7399457 | 0.106 | 0.354 | 0e+00 |
| Scimp | 0 | -3.1149380 | 0.015 | 0.142 | 0e+00 |
| Ccl2 | 0 | -4.3079631 | 0.015 | 0.142 | 0e+00 |
| Sp110 | 0 | -1.3571338 | 0.217 | 0.513 | 0e+00 |
| Pml | 0 | -2.1044100 | 0.106 | 0.336 | 0e+00 |
| Adar | 0 | -0.9879565 | 0.089 | 0.319 | 0e+00 |
| Cst7 | 0 | -3.0200531 | 0.089 | 0.310 | 0e+00 |
| Nmi | 0 | -1.2919726 | 0.074 | 0.292 | 0e+00 |
| Phf11 | 0 | -1.5011940 | 0.008 | 0.106 | 0e+00 |
| H2-D1 | 0 | -0.9590311 | 0.706 | 0.903 | 0e+00 |
| Oas1b | 0 | -1.8027668 | 0.060 | 0.257 | 0e+00 |
| Trim30c | 0 | -3.5829729 | 0.006 | 0.097 | 1e-07 |
| H2-Q6 | 0 | -2.6144165 | 0.217 | 0.487 | 1e-07 |
| Cd52 | 0 | -1.0951126 | 0.292 | 0.628 | 2e-07 |
| Psme2b | 0 | -1.6675677 | 0.170 | 0.442 | 2e-07 |
| Ogfr | 0 | -1.6458533 | 0.074 | 0.274 | 3e-07 |
| Marchf5 | 0 | -1.9246377 | 0.053 | 0.230 | 4e-07 |
Microglia1_vs_Microglia4_comorbid
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Ifit3 | 0 | -7.6836575 | 0.035 | 0.628 | 0e+00 |
| Rtp4 | 0 | -3.4269783 | 0.093 | 0.717 | 0e+00 |
| Ifit2 | 0 | -5.7226144 | 0.020 | 0.425 | 0e+00 |
| Ifi206 | 0 | -5.9016986 | 0.005 | 0.319 | 0e+00 |
| Irf7 | 0 | -5.2595288 | 0.020 | 0.398 | 0e+00 |
| Oas2 | 0 | -6.9393210 | 0.009 | 0.327 | 0e+00 |
| Ccl12 | 0 | -4.0601690 | 0.134 | 0.690 | 0e+00 |
| Ifitm3 | 0 | -4.0940045 | 0.078 | 0.566 | 0e+00 |
| Oas1a | 0 | -3.7958610 | 0.039 | 0.460 | 0e+00 |
| Oasl2 | 0 | -6.6386633 | 0.151 | 0.673 | 0e+00 |
| Mx1 | 0 | -5.7190001 | 0.071 | 0.522 | 0e+00 |
| Usp18 | 0 | -4.2357222 | 0.060 | 0.504 | 0e+00 |
| Stat1 | 0 | -2.9876200 | 0.255 | 0.823 | 0e+00 |
| Ifi27l2a | 0 | -3.2639683 | 0.074 | 0.540 | 0e+00 |
| Tgtp2 | 0 | -5.9720180 | 0.034 | 0.389 | 0e+00 |
| Ifi211 | 0 | -6.0183554 | 0.009 | 0.283 | 0e+00 |
| Ifi207 | 0 | -5.7326783 | 0.025 | 0.354 | 0e+00 |
| Ifit3b | 0 | -8.0293608 | 0.081 | 0.504 | 0e+00 |
| Oas1g | 0 | -3.4631047 | 0.039 | 0.407 | 0e+00 |
| Nlrc5 | 0 | -2.8635630 | 0.045 | 0.425 | 0e+00 |
| Mx2 | 0 | -4.5855953 | 0.019 | 0.310 | 0e+00 |
| Zbp1 | 0 | -4.9466230 | 0.035 | 0.363 | 0e+00 |
| Lgals3bp | 0 | -2.5751171 | 0.315 | 0.814 | 0e+00 |
| Rnf213 | 0 | -2.5193816 | 0.139 | 0.628 | 0e+00 |
| Phf11b | 0 | -3.8510101 | 0.045 | 0.389 | 0e+00 |
| Trim30a | 0 | -1.9922470 | 0.230 | 0.726 | 0e+00 |
| Ifi209 | 0 | -3.6612821 | 0.088 | 0.469 | 0e+00 |
| Trex1 | 0 | -2.3489345 | 0.128 | 0.575 | 0e+00 |
| Phf11a | 0 | -5.1883581 | 0.039 | 0.345 | 0e+00 |
| Iigp1 | 0 | -5.3856932 | 0.141 | 0.558 | 0e+00 |
| Ifit1 | 0 | -6.5414183 | 0.051 | 0.363 | 0e+00 |
| Iigp1c | 0 | -3.4666543 | 0.189 | 0.602 | 0e+00 |
| Fgl2 | 0 | -2.9387304 | 0.076 | 0.442 | 0e+00 |
| Trim30d | 0 | -2.1350605 | 0.148 | 0.584 | 0e+00 |
| Ifi204 | 0 | -2.9241664 | 0.307 | 0.726 | 0e+00 |
| Helz2 | 0 | -9.1157491 | 0.008 | 0.195 | 0e+00 |
| Parp12 | 0 | -2.4273847 | 0.075 | 0.416 | 0e+00 |
| Rsad2 | 0 | -6.8488297 | 0.044 | 0.319 | 0e+00 |
| Gvin1 | 0 | -2.1665846 | 0.161 | 0.593 | 0e+00 |
| Cmpk2 | 0 | -5.1802465 | 0.004 | 0.159 | 0e+00 |
| Tor3a | 0 | -1.4478519 | 0.121 | 0.496 | 0e+00 |
| Ifi213 | 0 | -5.6531206 | 0.156 | 0.513 | 0e+00 |
| Slfn2 | 0 | -3.1617971 | 0.128 | 0.487 | 0e+00 |
| Bst2 | 0 | -2.0339628 | 0.166 | 0.558 | 0e+00 |
| Gvin2 | 0 | -2.3457184 | 0.180 | 0.593 | 0e+00 |
| Oasl1 | 0 | -8.3848299 | 0.010 | 0.177 | 0e+00 |
| Samd9l | 0 | -2.3838732 | 0.030 | 0.257 | 0e+00 |
| Isg15 | 0 | -3.6217003 | 0.133 | 0.460 | 0e+00 |
| Phf11d | 0 | -2.8198216 | 0.114 | 0.442 | 0e+00 |
| Ifi208 | 0 | -3.6570245 | 0.130 | 0.469 | 0e+00 |
| Slfn8 | 0 | -1.8602422 | 0.267 | 0.673 | 0e+00 |
| Parp9 | 0 | -2.2835738 | 0.085 | 0.389 | 0e+00 |
| Ifi214 | 0 | -3.2801761 | 0.123 | 0.451 | 0e+00 |
| Parp14 | 0 | -2.7384079 | 0.196 | 0.531 | 0e+00 |
| Ifi205 | 0 | -4.1872323 | 0.010 | 0.159 | 0e+00 |
| Sp100 | 0 | -2.8012144 | 0.287 | 0.611 | 0e+00 |
| Herc6 | 0 | -2.6516256 | 0.358 | 0.681 | 0e+00 |
| Gvin-ps7 | 0 | -2.2710598 | 0.207 | 0.558 | 0e+00 |
| Xaf1 | 0 | -2.4885923 | 0.406 | 0.708 | 0e+00 |
| Psmb8 | 0 | -1.4728430 | 0.308 | 0.690 | 0e+00 |
| Ly6a | 0 | -2.7870305 | 0.024 | 0.204 | 0e+00 |
| Etnk1 | 0 | -1.5101625 | 0.218 | 0.575 | 0e+00 |
| Fcgr1 | 0 | -1.1017639 | 0.477 | 0.850 | 0e+00 |
| Axl | 0 | -2.5188740 | 0.073 | 0.327 | 0e+00 |
| Irgm1 | 0 | -2.5222329 | 0.234 | 0.549 | 0e+00 |
| Ifih1 | 0 | -1.8123811 | 0.103 | 0.381 | 0e+00 |
| Nampt | 0 | -2.3772952 | 0.056 | 0.283 | 0e+00 |
| Ly6e | 0 | -1.2520987 | 0.680 | 0.912 | 0e+00 |
| Ifi35 | 0 | -1.5997760 | 0.116 | 0.416 | 0e+00 |
| Gbp9 | 0 | -1.4750605 | 0.056 | 0.283 | 0e+00 |
| Slfn5 | 0 | -2.1892455 | 0.421 | 0.717 | 0e+00 |
| Znfx1 | 0 | -1.6048796 | 0.194 | 0.522 | 0e+00 |
| Ddx60 | 0 | -1.8121202 | 0.109 | 0.381 | 0e+00 |
| B2m | 0 | -0.6923878 | 0.949 | 1.000 | 0e+00 |
| Isg20 | 0 | -1.5801535 | 0.028 | 0.195 | 0e+00 |
| Dhx58 | 0 | -3.0240630 | 0.134 | 0.398 | 0e+00 |
| Dtx3l | 0 | -1.5922911 | 0.363 | 0.690 | 0e+00 |
| Sdc3 | 0 | -2.3546565 | 0.069 | 0.292 | 0e+00 |
| Ifi47 | 0 | -6.8057973 | 0.004 | 0.097 | 0e+00 |
| Epsti1 | 0 | -1.6691286 | 0.089 | 0.336 | 0e+00 |
| Eif2ak2 | 0 | -1.1031130 | 0.494 | 0.779 | 0e+00 |
| Trafd1 | 0 | -1.5215331 | 0.190 | 0.496 | 0e+00 |
| Trem6l | 0 | -2.3008212 | 0.099 | 0.336 | 0e+00 |
| Tap1 | 0 | -1.7399457 | 0.106 | 0.354 | 0e+00 |
| Scimp | 0 | -3.1149380 | 0.015 | 0.142 | 0e+00 |
| Ccl2 | 0 | -4.3079631 | 0.015 | 0.142 | 0e+00 |
| Sp110 | 0 | -1.3571338 | 0.217 | 0.513 | 0e+00 |
| Pml | 0 | -2.1044100 | 0.106 | 0.336 | 0e+00 |
| Adar | 0 | -0.9879565 | 0.089 | 0.319 | 0e+00 |
| Cst7 | 0 | -3.0200531 | 0.089 | 0.310 | 0e+00 |
| Nmi | 0 | -1.2919726 | 0.074 | 0.292 | 0e+00 |
| Phf11 | 0 | -1.5011940 | 0.008 | 0.106 | 0e+00 |
| H2-D1 | 0 | -0.9590311 | 0.706 | 0.903 | 0e+00 |
| Oas1b | 0 | -1.8027668 | 0.060 | 0.257 | 0e+00 |
| Trim30c | 0 | -3.5829729 | 0.006 | 0.097 | 1e-07 |
| H2-Q6 | 0 | -2.6144165 | 0.217 | 0.487 | 1e-07 |
| Cd52 | 0 | -1.0951126 | 0.292 | 0.628 | 2e-07 |
| Psme2b | 0 | -1.6675677 | 0.170 | 0.442 | 2e-07 |
| Ogfr | 0 | -1.6458533 | 0.074 | 0.274 | 3e-07 |
| Marchf5 | 0 | -1.9246377 | 0.053 | 0.230 | 4e-07 |
Microglia1_vs_Microglia5
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| H2-Ab1 | 0.0e+00 | -9.1615935 | 0.026 | 0.904 | 0.0000000 |
| Cd74 | 0.0e+00 | -7.2748897 | 0.096 | 0.959 | 0.0000000 |
| H2-Eb1 | 0.0e+00 | -9.5285827 | 0.021 | 0.630 | 0.0000000 |
| H2-Aa | 0.0e+00 | -10.3520212 | 0.071 | 0.712 | 0.0000000 |
| H2-D1 | 0.0e+00 | -1.9011179 | 0.706 | 0.959 | 0.0000000 |
| H2-K1 | 0.0e+00 | -1.3779921 | 0.657 | 0.932 | 0.0000000 |
| Usp12 | 0.0e+00 | -1.9021436 | 0.105 | 0.425 | 0.0000000 |
| H2-Oa | 0.0e+00 | -2.1263695 | 0.076 | 0.356 | 0.0000000 |
| Nbl1 | 0.0e+00 | -8.9196769 | 0.003 | 0.096 | 0.0000000 |
| Wfdc17 | 0.0e+00 | -6.3884755 | 0.003 | 0.096 | 0.0000000 |
| Pfkm | 0.0e+00 | -3.3132871 | 0.001 | 0.082 | 0.0000000 |
| Ccl3 | 0.0e+00 | -1.3450746 | 0.048 | 0.260 | 0.0000000 |
| Trac | 0.0e+00 | 2.2298370 | 0.869 | 0.644 | 0.0000001 |
| Itgax | 0.0e+00 | -2.6567752 | 0.033 | 0.205 | 0.0000003 |
| Vwa3b | 0.0e+00 | -3.8470492 | 0.001 | 0.068 | 0.0000005 |
| H2-Q7 | 0.0e+00 | -3.2320335 | 0.310 | 0.603 | 0.0000008 |
| Arfgef3 | 0.0e+00 | 1.5602380 | 0.874 | 0.658 | 0.0000009 |
| Axl | 0.0e+00 | -1.9759252 | 0.073 | 0.301 | 0.0000012 |
| Capg | 0.0e+00 | -2.5076612 | 0.063 | 0.274 | 0.0000016 |
| Ccl6 | 0.0e+00 | -1.9626530 | 0.194 | 0.507 | 0.0000031 |
| Ank | 0.0e+00 | -2.8611782 | 0.066 | 0.274 | 0.0000031 |
| Eif2a | 0.0e+00 | 1.5886406 | 0.937 | 0.808 | 0.0000037 |
| Baiap2l2 | 0.0e+00 | -5.5464903 | 0.006 | 0.096 | 0.0000042 |
| Tspo | 0.0e+00 | -1.1561638 | 0.118 | 0.397 | 0.0000045 |
| Tsc22d1 | 0.0e+00 | -4.0387725 | 0.016 | 0.137 | 0.0000097 |
| Cst7 | 0.0e+00 | -4.2240302 | 0.089 | 0.301 | 0.0000102 |
| Cox6a2 | 0.0e+00 | -1.7035712 | 0.024 | 0.164 | 0.0000110 |
| Pax6 | 0.0e+00 | 1.6032731 | 0.846 | 0.671 | 0.0000178 |
| H2-Q6 | 0.0e+00 | -3.1471948 | 0.217 | 0.493 | 0.0000195 |
| Ifi27l2a | 0.0e+00 | -1.5391876 | 0.074 | 0.288 | 0.0000257 |
| H2-T23 | 0.0e+00 | -1.3357062 | 0.526 | 0.808 | 0.0000321 |
| Cep290 | 0.0e+00 | 1.5055324 | 0.916 | 0.712 | 0.0000341 |
| Hpse | 0.0e+00 | -8.4965199 | 0.005 | 0.082 | 0.0000413 |
| Clec7a | 0.0e+00 | -2.5944974 | 0.081 | 0.288 | 0.0000602 |
| B2m | 0.0e+00 | -0.7872743 | 0.949 | 0.986 | 0.0000660 |
| Or52m1 | 0.0e+00 | 2.1355512 | 0.807 | 0.575 | 0.0000800 |
| Ift20 | 0.0e+00 | 1.2946543 | 0.872 | 0.726 | 0.0000819 |
| Vmn1r13 | 0.0e+00 | 1.4517681 | 0.914 | 0.726 | 0.0000819 |
| Atp1a3 | 0.0e+00 | -2.6780174 | 0.069 | 0.260 | 0.0000824 |
| Colec10 | 0.0e+00 | -5.2619825 | 0.001 | 0.055 | 0.0001118 |
| Vmn1r-ps73 | 0.0e+00 | -1.3940162 | 0.001 | 0.055 | 0.0001143 |
| Ramp1 | 0.0e+00 | -1.3997755 | 0.080 | 0.288 | 0.0001263 |
| Mtss1 | 0.0e+00 | 1.4701886 | 0.756 | 0.507 | 0.0001304 |
| Ly6e | 0.0e+00 | -1.1252784 | 0.680 | 0.863 | 0.0001475 |
| Lancl2 | 0.0e+00 | -7.3231896 | 0.000 | 0.041 | 0.0001560 |
| Prr15 | 0.0e+00 | 3.8659262 | 0.837 | 0.616 | 0.0001726 |
| AI593442 | 0.0e+00 | 1.6821530 | 0.747 | 0.466 | 0.0002149 |
| Ctsd | 0.0e+00 | -0.8894259 | 0.954 | 0.973 | 0.0002761 |
| Syngr1 | 0.0e+00 | -1.0531995 | 0.482 | 0.753 | 0.0003254 |
| H2-M3 | 0.0e+00 | -1.3301784 | 0.153 | 0.411 | 0.0003446 |
| Rps16-ps2 | 0.0e+00 | -0.9725873 | 0.255 | 0.575 | 0.0004555 |
| Fgl2 | 0.0e+00 | -1.6657788 | 0.076 | 0.274 | 0.0005406 |
| Lipe | 1.0e-07 | 1.4223459 | 0.935 | 0.836 | 0.0010270 |
| Taf6l | 1.0e-07 | -1.6705182 | 0.048 | 0.205 | 0.0011975 |
| Cux2 | 1.0e-07 | 1.3261330 | 0.924 | 0.795 | 0.0013095 |
| Malat1 | 1.0e-07 | 0.5731738 | 0.987 | 0.973 | 0.0016188 |
| Bphl | 1.0e-07 | -2.5480556 | 0.028 | 0.151 | 0.0020212 |
| Tyrobp | 1.0e-07 | -1.1456426 | 0.815 | 0.973 | 0.0023687 |
| Spp1 | 2.0e-07 | -7.3747631 | 0.015 | 0.110 | 0.0027070 |
| Pgrmc2 | 2.0e-07 | -1.7936901 | 0.039 | 0.178 | 0.0035689 |
| Dcstamp | 2.0e-07 | -4.6882512 | 0.003 | 0.055 | 0.0036220 |
| Lrrc8b | 2.0e-07 | -1.9467945 | 0.003 | 0.055 | 0.0037559 |
| Stx7 | 2.0e-07 | -0.8949923 | 0.419 | 0.712 | 0.0038344 |
| Dido1 | 3.0e-07 | 0.8936436 | 0.907 | 0.712 | 0.0039928 |
| Oc90 | 3.0e-07 | -3.0472587 | 0.003 | 0.055 | 0.0040382 |
| Lgals3bp | 3.0e-07 | -1.7109838 | 0.315 | 0.548 | 0.0047205 |
| Dpf1 | 3.0e-07 | 1.3786950 | 0.682 | 0.452 | 0.0052532 |
| Mif | 4.0e-07 | -1.0478043 | 0.149 | 0.384 | 0.0056331 |
| Slc2a1 | 4.0e-07 | -2.3835466 | 0.066 | 0.233 | 0.0059094 |
| Ctsb | 4.0e-07 | -0.9025466 | 0.876 | 0.959 | 0.0069171 |
| Slc25a4 | 5.0e-07 | -0.6885710 | 0.164 | 0.411 | 0.0073550 |
| Sem1 | 5.0e-07 | -0.5658439 | 0.168 | 0.425 | 0.0077894 |
| AW112010 | 6.0e-07 | -1.5070601 | 0.066 | 0.233 | 0.0088998 |
| Or8b44 | 7.0e-07 | 2.7349923 | 0.896 | 0.726 | 0.0104745 |
| Tmsb10 | 7.0e-07 | -0.2382261 | 0.194 | 0.466 | 0.0107471 |
| Dnajc12 | 7.0e-07 | -1.2350834 | 0.280 | 0.534 | 0.0109490 |
| Il3ra | 8.0e-07 | -2.2883458 | 0.009 | 0.082 | 0.0120258 |
| Selenom | 8.0e-07 | -2.8357614 | 0.009 | 0.082 | 0.0123148 |
| Stt3b | 8.0e-07 | -1.1627459 | 0.080 | 0.260 | 0.0128357 |
| Amy1 | 8.0e-07 | -1.9939308 | 0.009 | 0.082 | 0.0129128 |
| Lratd1 | 9.0e-07 | 2.1995711 | 0.597 | 0.329 | 0.0136850 |
| Or14c41 | 9.0e-07 | 0.8980247 | 0.804 | 0.575 | 0.0139532 |
| H2-DMa | 9.0e-07 | -0.9792104 | 0.323 | 0.589 | 0.0148482 |
| Ifi35 | 1.1e-06 | -0.8686203 | 0.116 | 0.329 | 0.0175605 |
| Parp12 | 1.2e-06 | -0.7657879 | 0.075 | 0.247 | 0.0191328 |
| Tmem229b | 1.2e-06 | -3.3582690 | 0.079 | 0.247 | 0.0194981 |
| Zbtb44 | 1.3e-06 | 1.6966785 | 0.889 | 0.644 | 0.0209893 |
| Ly86 | 1.3e-06 | -0.5742444 | 0.847 | 0.986 | 0.0213224 |
| Mamdc2 | 1.4e-06 | -5.5439934 | 0.001 | 0.041 | 0.0224555 |
| Klf2 | 1.4e-06 | -5.9602405 | 0.001 | 0.041 | 0.0224555 |
| Rpl36a-ps2 | 1.4e-06 | -0.4064255 | 0.163 | 0.384 | 0.0230264 |
| Mn1 | 1.5e-06 | 1.5169760 | 0.586 | 0.329 | 0.0231627 |
| Cfap221 | 1.5e-06 | -3.7805722 | 0.001 | 0.041 | 0.0234089 |
| Gpx4 | 1.5e-06 | -0.8000959 | 0.200 | 0.466 | 0.0234724 |
| Egln3 | 1.6e-06 | -4.6957650 | 0.006 | 0.068 | 0.0257964 |
| Tap1 | 1.6e-06 | -1.0804145 | 0.106 | 0.301 | 0.0260712 |
| Setd6 | 1.8e-06 | -2.5829705 | 0.006 | 0.068 | 0.0279082 |
| Cd200r4 | 1.8e-06 | -1.5822023 | 0.006 | 0.068 | 0.0286483 |
| Chst12 | 1.9e-06 | -0.9974524 | 0.069 | 0.233 | 0.0308791 |
| Rpl14-ps1 | 2.4e-06 | -1.3172338 | 0.074 | 0.233 | 0.0388496 |
Microglia1_vs_Microglia5_comorbid
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| H2-Ab1 | 0.0e+00 | -9.1615935 | 0.026 | 0.904 | 0.0000000 |
| Cd74 | 0.0e+00 | -7.2748897 | 0.096 | 0.959 | 0.0000000 |
| H2-Eb1 | 0.0e+00 | -9.5285827 | 0.021 | 0.630 | 0.0000000 |
| H2-Aa | 0.0e+00 | -10.3520212 | 0.071 | 0.712 | 0.0000000 |
| H2-D1 | 0.0e+00 | -1.9011179 | 0.706 | 0.959 | 0.0000000 |
| H2-K1 | 0.0e+00 | -1.3779921 | 0.657 | 0.932 | 0.0000000 |
| Usp12 | 0.0e+00 | -1.9021436 | 0.105 | 0.425 | 0.0000000 |
| H2-Oa | 0.0e+00 | -2.1263695 | 0.076 | 0.356 | 0.0000000 |
| Nbl1 | 0.0e+00 | -8.9196769 | 0.003 | 0.096 | 0.0000000 |
| Wfdc17 | 0.0e+00 | -6.3884755 | 0.003 | 0.096 | 0.0000000 |
| Pfkm | 0.0e+00 | -3.3132871 | 0.001 | 0.082 | 0.0000000 |
| Ccl3 | 0.0e+00 | -1.3450746 | 0.048 | 0.260 | 0.0000000 |
| Trac | 0.0e+00 | 2.2298370 | 0.869 | 0.644 | 0.0000001 |
| Itgax | 0.0e+00 | -2.6567752 | 0.033 | 0.205 | 0.0000003 |
| Vwa3b | 0.0e+00 | -3.8470492 | 0.001 | 0.068 | 0.0000005 |
| H2-Q7 | 0.0e+00 | -3.2320335 | 0.310 | 0.603 | 0.0000008 |
| Arfgef3 | 0.0e+00 | 1.5602380 | 0.874 | 0.658 | 0.0000009 |
| Axl | 0.0e+00 | -1.9759252 | 0.073 | 0.301 | 0.0000012 |
| Capg | 0.0e+00 | -2.5076612 | 0.063 | 0.274 | 0.0000016 |
| Ccl6 | 0.0e+00 | -1.9626530 | 0.194 | 0.507 | 0.0000031 |
| Ank | 0.0e+00 | -2.8611782 | 0.066 | 0.274 | 0.0000031 |
| Eif2a | 0.0e+00 | 1.5886406 | 0.937 | 0.808 | 0.0000037 |
| Baiap2l2 | 0.0e+00 | -5.5464903 | 0.006 | 0.096 | 0.0000042 |
| Tspo | 0.0e+00 | -1.1561638 | 0.118 | 0.397 | 0.0000045 |
| Tsc22d1 | 0.0e+00 | -4.0387725 | 0.016 | 0.137 | 0.0000097 |
| Cst7 | 0.0e+00 | -4.2240302 | 0.089 | 0.301 | 0.0000102 |
| Cox6a2 | 0.0e+00 | -1.7035712 | 0.024 | 0.164 | 0.0000110 |
| Pax6 | 0.0e+00 | 1.6032731 | 0.846 | 0.671 | 0.0000178 |
| H2-Q6 | 0.0e+00 | -3.1471948 | 0.217 | 0.493 | 0.0000195 |
| Ifi27l2a | 0.0e+00 | -1.5391876 | 0.074 | 0.288 | 0.0000257 |
| H2-T23 | 0.0e+00 | -1.3357062 | 0.526 | 0.808 | 0.0000321 |
| Cep290 | 0.0e+00 | 1.5055324 | 0.916 | 0.712 | 0.0000341 |
| Hpse | 0.0e+00 | -8.4965199 | 0.005 | 0.082 | 0.0000413 |
| Clec7a | 0.0e+00 | -2.5944974 | 0.081 | 0.288 | 0.0000602 |
| B2m | 0.0e+00 | -0.7872743 | 0.949 | 0.986 | 0.0000660 |
| Or52m1 | 0.0e+00 | 2.1355512 | 0.807 | 0.575 | 0.0000800 |
| Ift20 | 0.0e+00 | 1.2946543 | 0.872 | 0.726 | 0.0000819 |
| Vmn1r13 | 0.0e+00 | 1.4517681 | 0.914 | 0.726 | 0.0000819 |
| Atp1a3 | 0.0e+00 | -2.6780174 | 0.069 | 0.260 | 0.0000824 |
| Colec10 | 0.0e+00 | -5.2619825 | 0.001 | 0.055 | 0.0001118 |
| Vmn1r-ps73 | 0.0e+00 | -1.3940162 | 0.001 | 0.055 | 0.0001143 |
| Ramp1 | 0.0e+00 | -1.3997755 | 0.080 | 0.288 | 0.0001263 |
| Mtss1 | 0.0e+00 | 1.4701886 | 0.756 | 0.507 | 0.0001304 |
| Ly6e | 0.0e+00 | -1.1252784 | 0.680 | 0.863 | 0.0001475 |
| Lancl2 | 0.0e+00 | -7.3231896 | 0.000 | 0.041 | 0.0001560 |
| Prr15 | 0.0e+00 | 3.8659262 | 0.837 | 0.616 | 0.0001726 |
| AI593442 | 0.0e+00 | 1.6821530 | 0.747 | 0.466 | 0.0002149 |
| Ctsd | 0.0e+00 | -0.8894259 | 0.954 | 0.973 | 0.0002761 |
| Syngr1 | 0.0e+00 | -1.0531995 | 0.482 | 0.753 | 0.0003254 |
| H2-M3 | 0.0e+00 | -1.3301784 | 0.153 | 0.411 | 0.0003446 |
| Rps16-ps2 | 0.0e+00 | -0.9725873 | 0.255 | 0.575 | 0.0004555 |
| Fgl2 | 0.0e+00 | -1.6657788 | 0.076 | 0.274 | 0.0005406 |
| Lipe | 1.0e-07 | 1.4223459 | 0.935 | 0.836 | 0.0010270 |
| Taf6l | 1.0e-07 | -1.6705182 | 0.048 | 0.205 | 0.0011975 |
| Cux2 | 1.0e-07 | 1.3261330 | 0.924 | 0.795 | 0.0013095 |
| Malat1 | 1.0e-07 | 0.5731738 | 0.987 | 0.973 | 0.0016188 |
| Bphl | 1.0e-07 | -2.5480556 | 0.028 | 0.151 | 0.0020212 |
| Tyrobp | 1.0e-07 | -1.1456426 | 0.815 | 0.973 | 0.0023687 |
| Spp1 | 2.0e-07 | -7.3747631 | 0.015 | 0.110 | 0.0027070 |
| Pgrmc2 | 2.0e-07 | -1.7936901 | 0.039 | 0.178 | 0.0035689 |
| Dcstamp | 2.0e-07 | -4.6882512 | 0.003 | 0.055 | 0.0036220 |
| Lrrc8b | 2.0e-07 | -1.9467945 | 0.003 | 0.055 | 0.0037559 |
| Stx7 | 2.0e-07 | -0.8949923 | 0.419 | 0.712 | 0.0038344 |
| Dido1 | 3.0e-07 | 0.8936436 | 0.907 | 0.712 | 0.0039928 |
| Oc90 | 3.0e-07 | -3.0472587 | 0.003 | 0.055 | 0.0040382 |
| Lgals3bp | 3.0e-07 | -1.7109838 | 0.315 | 0.548 | 0.0047205 |
| Dpf1 | 3.0e-07 | 1.3786950 | 0.682 | 0.452 | 0.0052532 |
| Mif | 4.0e-07 | -1.0478043 | 0.149 | 0.384 | 0.0056331 |
| Slc2a1 | 4.0e-07 | -2.3835466 | 0.066 | 0.233 | 0.0059094 |
| Ctsb | 4.0e-07 | -0.9025466 | 0.876 | 0.959 | 0.0069171 |
| Slc25a4 | 5.0e-07 | -0.6885710 | 0.164 | 0.411 | 0.0073550 |
| Sem1 | 5.0e-07 | -0.5658439 | 0.168 | 0.425 | 0.0077894 |
| AW112010 | 6.0e-07 | -1.5070601 | 0.066 | 0.233 | 0.0088998 |
| Or8b44 | 7.0e-07 | 2.7349923 | 0.896 | 0.726 | 0.0104745 |
| Tmsb10 | 7.0e-07 | -0.2382261 | 0.194 | 0.466 | 0.0107471 |
| Dnajc12 | 7.0e-07 | -1.2350834 | 0.280 | 0.534 | 0.0109490 |
| Il3ra | 8.0e-07 | -2.2883458 | 0.009 | 0.082 | 0.0120258 |
| Selenom | 8.0e-07 | -2.8357614 | 0.009 | 0.082 | 0.0123148 |
| Stt3b | 8.0e-07 | -1.1627459 | 0.080 | 0.260 | 0.0128357 |
| Amy1 | 8.0e-07 | -1.9939308 | 0.009 | 0.082 | 0.0129128 |
| Lratd1 | 9.0e-07 | 2.1995711 | 0.597 | 0.329 | 0.0136850 |
| Or14c41 | 9.0e-07 | 0.8980247 | 0.804 | 0.575 | 0.0139532 |
| H2-DMa | 9.0e-07 | -0.9792104 | 0.323 | 0.589 | 0.0148482 |
| Ifi35 | 1.1e-06 | -0.8686203 | 0.116 | 0.329 | 0.0175605 |
| Parp12 | 1.2e-06 | -0.7657879 | 0.075 | 0.247 | 0.0191328 |
| Tmem229b | 1.2e-06 | -3.3582690 | 0.079 | 0.247 | 0.0194981 |
| Zbtb44 | 1.3e-06 | 1.6966785 | 0.889 | 0.644 | 0.0209893 |
| Ly86 | 1.3e-06 | -0.5742444 | 0.847 | 0.986 | 0.0213224 |
| Mamdc2 | 1.4e-06 | -5.5439934 | 0.001 | 0.041 | 0.0224555 |
| Klf2 | 1.4e-06 | -5.9602405 | 0.001 | 0.041 | 0.0224555 |
| Rpl36a-ps2 | 1.4e-06 | -0.4064255 | 0.163 | 0.384 | 0.0230264 |
| Mn1 | 1.5e-06 | 1.5169760 | 0.586 | 0.329 | 0.0231627 |
| Cfap221 | 1.5e-06 | -3.7805722 | 0.001 | 0.041 | 0.0234089 |
| Gpx4 | 1.5e-06 | -0.8000959 | 0.200 | 0.466 | 0.0234724 |
| Egln3 | 1.6e-06 | -4.6957650 | 0.006 | 0.068 | 0.0257964 |
| Tap1 | 1.6e-06 | -1.0804145 | 0.106 | 0.301 | 0.0260712 |
| Setd6 | 1.8e-06 | -2.5829705 | 0.006 | 0.068 | 0.0279082 |
| Cd200r4 | 1.8e-06 | -1.5822023 | 0.006 | 0.068 | 0.0286483 |
| Chst12 | 1.9e-06 | -0.9974524 | 0.069 | 0.233 | 0.0308791 |
| Rpl14-ps1 | 2.4e-06 | -1.3172338 | 0.074 | 0.233 | 0.0388496 |
Microglia2_vs_Microglia3
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-46.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Apoe | 0 | 3.9199970 | 0.937 | 0.374 | 0 |
| Ctsd | 0 | 2.2925635 | 1.000 | 0.793 | 0 |
| Ctsb | 0 | 2.1141633 | 0.993 | 0.586 | 0 |
| Ctsz | 0 | 2.0452690 | 0.987 | 0.552 | 0 |
| Lyz2 | 0 | 2.4068165 | 0.921 | 0.320 | 0 |
| H2-D1 | 0 | 2.4418500 | 0.941 | 0.355 | 0 |
| Cd9 | 0 | 2.0479351 | 0.969 | 0.537 | 0 |
| Serpine2 | 0 | 2.5729102 | 0.928 | 0.369 | 0 |
| Fth1 | 0 | 1.6678635 | 0.983 | 0.581 | 0 |
| Tyrobp | 0 | 2.1800743 | 0.980 | 0.562 | 0 |
| Ftl1 | 0 | 1.7163234 | 0.976 | 0.517 | 0 |
| Cst7 | 0 | 6.7126878 | 0.705 | 0.074 | 0 |
| Cd63 | 0 | 1.9262651 | 0.893 | 0.281 | 0 |
| Rps2 | 0 | 2.5952528 | 0.786 | 0.128 | 0 |
| Cd68 | 0 | 1.2503386 | 0.932 | 0.399 | 0 |
| Lgals3bp | 0 | 3.3596085 | 0.758 | 0.158 | 0 |
| Clec7a | 0 | 2.5519793 | 0.668 | 0.054 | 0 |
| Ctsa | 0 | 1.2311744 | 0.959 | 0.502 | 0 |
| Uba52 | 0 | 0.1121277 | 0.812 | 0.167 | 0 |
| Vmn1r13 | 0 | -4.9582871 | 0.758 | 0.946 | 0 |
| Syngr1 | 0 | 2.6954257 | 0.810 | 0.256 | 0 |
| Rpl18a | 0 | 1.1367984 | 0.952 | 0.389 | 0 |
| Trem2 | 0 | 1.4883107 | 0.963 | 0.527 | 0 |
| Lpl | 0 | 4.1970190 | 0.825 | 0.271 | 0 |
| Or8b44 | 0 | -6.4928759 | 0.707 | 0.921 | 0 |
| Atp6v0c | 0 | 1.7958977 | 0.838 | 0.296 | 0 |
| Lipe | 0 | -4.3434442 | 0.830 | 0.975 | 0 |
| H2-K1 | 0 | 1.7550056 | 0.900 | 0.389 | 0 |
| Uba52rt | 0 | 0.1782772 | 0.755 | 0.153 | 0 |
| Npc2 | 0 | 1.1769112 | 0.926 | 0.429 | 0 |
| Hexa | 0 | 1.4214090 | 0.904 | 0.409 | 0 |
| Grn | 0 | 1.4039361 | 0.945 | 0.473 | 0 |
| Ctsl | 0 | 1.2654097 | 0.969 | 0.591 | 0 |
| Rpl41 | 0 | 0.1334857 | 0.930 | 0.330 | 0 |
| Tpt1 | 0 | 1.7310788 | 0.825 | 0.276 | 0 |
| Ly86 | 0 | 1.0423897 | 0.965 | 0.512 | 0 |
| Gusb | 0 | 1.4721025 | 0.793 | 0.271 | 0 |
| Gapdh | 0 | 0.1362397 | 0.841 | 0.320 | 0 |
| Rplp0 | 0 | 1.6586937 | 0.852 | 0.315 | 0 |
| Ctsh | 0 | 0.2664088 | 0.893 | 0.379 | 0 |
| Aldoa | 0 | 2.2642062 | 0.784 | 0.246 | 0 |
| Eef1a1 | 0 | 0.8877638 | 0.989 | 0.660 | 0 |
| Hspa8 | 0 | 1.2737738 | 0.900 | 0.374 | 0 |
| C1qc | 0 | 1.2484864 | 0.996 | 0.729 | 0 |
| C1qa | 0 | 1.2736360 | 0.998 | 0.675 | 0 |
| Rps24 | 0 | 0.2889303 | 0.865 | 0.261 | 0 |
| Mif | 0 | 3.7970152 | 0.605 | 0.054 | 0 |
| Trac | 0 | -5.3396713 | 0.568 | 0.823 | 0 |
| Mpeg1 | 0 | 1.1410246 | 0.924 | 0.404 | 0 |
| Sh3bgrl3 | 0 | 1.3232246 | 0.745 | 0.167 | 0 |
| Rps9 | 0 | 1.0530632 | 0.884 | 0.335 | 0 |
| Rps19 | 0 | 0.7872978 | 0.871 | 0.310 | 0 |
| Rps16-ps2 | 0 | 2.3027221 | 0.701 | 0.128 | 0 |
| Pkm | 0 | 2.2779373 | 0.642 | 0.094 | 0 |
| Eif2a | 0 | -3.9020174 | 0.858 | 0.941 | 0 |
| Serf2 | 0 | 0.8183050 | 0.784 | 0.182 | 0 |
| Rpl13a | 0 | 1.0232587 | 0.917 | 0.355 | 0 |
| Axl | 0 | 8.9220958 | 0.533 | 0.020 | 0 |
| Rplp1 | 0 | 0.5833906 | 0.932 | 0.389 | 0 |
| Rps5 | 0 | 1.8679160 | 0.679 | 0.133 | 0 |
| Cux2 | 0 | -4.2456520 | 0.821 | 0.906 | 0 |
| Prdx1 | 0 | 1.0066697 | 0.755 | 0.227 | 0 |
| Plxdc2 | 0 | 1.6362229 | 0.843 | 0.384 | 0 |
| Rps18 | 0 | 1.0258005 | 0.865 | 0.300 | 0 |
| Cfl1 | 0 | 1.2196355 | 0.884 | 0.463 | 0 |
| Man2b1 | 0 | 0.9932871 | 0.886 | 0.399 | 0 |
| Cd52 | 0 | 0.6197818 | 0.738 | 0.187 | 0 |
| Rps6 | 0 | 0.7430137 | 0.779 | 0.197 | 0 |
| Rpl19 | 0 | 1.2497134 | 0.766 | 0.182 | 0 |
| Cox4i1 | 0 | 1.3180256 | 0.795 | 0.227 | 0 |
| Arfgef3 | 0 | -4.0098038 | 0.574 | 0.833 | 0 |
| Rps23-ps1 | 0 | 1.1017877 | 0.841 | 0.246 | 0 |
| Rps16 | 0 | 0.9529365 | 0.817 | 0.246 | 0 |
| Rplp2 | 0 | 0.7315401 | 0.793 | 0.207 | 0 |
| AU020206 | 0 | 2.4513427 | 0.688 | 0.172 | 0 |
| Rps28 | 0 | 1.0094138 | 0.891 | 0.291 | 0 |
| Laptm5 | 0 | 1.2047213 | 0.969 | 0.665 | 0 |
| Rpl3 | 0 | 1.4624131 | 0.773 | 0.232 | 0 |
| Ppt1 | 0 | 1.4212335 | 0.749 | 0.246 | 0 |
| Lamp1 | 0 | 0.4694796 | 0.915 | 0.448 | 0 |
| Creg1 | 0 | 0.9666021 | 0.773 | 0.251 | 0 |
| B2m | 0 | 0.9439195 | 0.989 | 0.734 | 0 |
| Hif1a | 0 | 3.1804196 | 0.587 | 0.074 | 0 |
| Rpl15 | 0 | 0.8104652 | 0.749 | 0.182 | 0 |
| Rpl13 | 0 | 0.7091759 | 0.880 | 0.305 | 0 |
| Rpl35a | 0 | 0.5728594 | 0.736 | 0.172 | 0 |
| Cd83 | 0 | 3.1097143 | 0.629 | 0.128 | 0 |
| Rpl32 | 0 | 0.0061385 | 0.882 | 0.305 | 0 |
| Rbm45 | 0 | -5.0699120 | 0.594 | 0.828 | 0 |
| Hsp90b1 | 0 | 0.6376631 | 0.841 | 0.330 | 0 |
| Pdia3 | 0 | 1.0331859 | 0.828 | 0.325 | 0 |
| Rps8 | 0 | 1.5908680 | 0.714 | 0.187 | 0 |
| Ctss | 0 | 0.9543452 | 1.000 | 0.847 | 0 |
| Ccl3 | 0 | 4.4857741 | 0.533 | 0.044 | 0 |
| Dnajb14 | 0 | 2.3303873 | 0.692 | 0.177 | 0 |
| Cadm1 | 0 | 1.7429086 | 0.651 | 0.143 | 0 |
| Gnas | 0 | 1.7107747 | 0.734 | 0.212 | 0 |
| Rpl10a | 0 | 0.2706754 | 0.801 | 0.261 | 0 |
| Psap | 0 | 0.9238396 | 0.985 | 0.626 | 0 |
| Rpl18 | 0 | 0.7048072 | 0.740 | 0.207 | 0 |
Microglia2_vs_Microglia3_comorbid
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-49.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Apoe | 0 | 3.9199970 | 0.937 | 0.374 | 0 |
| Ctsd | 0 | 2.2925635 | 1.000 | 0.793 | 0 |
| Ctsb | 0 | 2.1141633 | 0.993 | 0.586 | 0 |
| Ctsz | 0 | 2.0452690 | 0.987 | 0.552 | 0 |
| Lyz2 | 0 | 2.4068165 | 0.921 | 0.320 | 0 |
| H2-D1 | 0 | 2.4418500 | 0.941 | 0.355 | 0 |
| Cd9 | 0 | 2.0479351 | 0.969 | 0.537 | 0 |
| Serpine2 | 0 | 2.5729102 | 0.928 | 0.369 | 0 |
| Fth1 | 0 | 1.6678635 | 0.983 | 0.581 | 0 |
| Tyrobp | 0 | 2.1800743 | 0.980 | 0.562 | 0 |
| Ftl1 | 0 | 1.7163234 | 0.976 | 0.517 | 0 |
| Cst7 | 0 | 6.7126878 | 0.705 | 0.074 | 0 |
| Cd63 | 0 | 1.9262651 | 0.893 | 0.281 | 0 |
| Rps2 | 0 | 2.5952528 | 0.786 | 0.128 | 0 |
| Cd68 | 0 | 1.2503386 | 0.932 | 0.399 | 0 |
| Lgals3bp | 0 | 3.3596085 | 0.758 | 0.158 | 0 |
| Clec7a | 0 | 2.5519793 | 0.668 | 0.054 | 0 |
| Ctsa | 0 | 1.2311744 | 0.959 | 0.502 | 0 |
| Uba52 | 0 | 0.1121277 | 0.812 | 0.167 | 0 |
| Vmn1r13 | 0 | -4.9582871 | 0.758 | 0.946 | 0 |
| Syngr1 | 0 | 2.6954257 | 0.810 | 0.256 | 0 |
| Rpl18a | 0 | 1.1367984 | 0.952 | 0.389 | 0 |
| Trem2 | 0 | 1.4883107 | 0.963 | 0.527 | 0 |
| Lpl | 0 | 4.1970190 | 0.825 | 0.271 | 0 |
| Or8b44 | 0 | -6.4928759 | 0.707 | 0.921 | 0 |
| Atp6v0c | 0 | 1.7958977 | 0.838 | 0.296 | 0 |
| Lipe | 0 | -4.3434442 | 0.830 | 0.975 | 0 |
| H2-K1 | 0 | 1.7550056 | 0.900 | 0.389 | 0 |
| Uba52rt | 0 | 0.1782772 | 0.755 | 0.153 | 0 |
| Npc2 | 0 | 1.1769112 | 0.926 | 0.429 | 0 |
| Hexa | 0 | 1.4214090 | 0.904 | 0.409 | 0 |
| Grn | 0 | 1.4039361 | 0.945 | 0.473 | 0 |
| Ctsl | 0 | 1.2654097 | 0.969 | 0.591 | 0 |
| Rpl41 | 0 | 0.1334857 | 0.930 | 0.330 | 0 |
| Tpt1 | 0 | 1.7310788 | 0.825 | 0.276 | 0 |
| Ly86 | 0 | 1.0423897 | 0.965 | 0.512 | 0 |
| Gusb | 0 | 1.4721025 | 0.793 | 0.271 | 0 |
| Gapdh | 0 | 0.1362397 | 0.841 | 0.320 | 0 |
| Rplp0 | 0 | 1.6586937 | 0.852 | 0.315 | 0 |
| Ctsh | 0 | 0.2664088 | 0.893 | 0.379 | 0 |
| Aldoa | 0 | 2.2642062 | 0.784 | 0.246 | 0 |
| Eef1a1 | 0 | 0.8877638 | 0.989 | 0.660 | 0 |
| Hspa8 | 0 | 1.2737738 | 0.900 | 0.374 | 0 |
| C1qc | 0 | 1.2484864 | 0.996 | 0.729 | 0 |
| C1qa | 0 | 1.2736360 | 0.998 | 0.675 | 0 |
| Rps24 | 0 | 0.2889303 | 0.865 | 0.261 | 0 |
| Mif | 0 | 3.7970152 | 0.605 | 0.054 | 0 |
| Trac | 0 | -5.3396713 | 0.568 | 0.823 | 0 |
| Mpeg1 | 0 | 1.1410246 | 0.924 | 0.404 | 0 |
| Sh3bgrl3 | 0 | 1.3232246 | 0.745 | 0.167 | 0 |
| Rps9 | 0 | 1.0530632 | 0.884 | 0.335 | 0 |
| Rps19 | 0 | 0.7872978 | 0.871 | 0.310 | 0 |
| Rps16-ps2 | 0 | 2.3027221 | 0.701 | 0.128 | 0 |
| Pkm | 0 | 2.2779373 | 0.642 | 0.094 | 0 |
| Eif2a | 0 | -3.9020174 | 0.858 | 0.941 | 0 |
| Serf2 | 0 | 0.8183050 | 0.784 | 0.182 | 0 |
| Rpl13a | 0 | 1.0232587 | 0.917 | 0.355 | 0 |
| Axl | 0 | 8.9220958 | 0.533 | 0.020 | 0 |
| Rplp1 | 0 | 0.5833906 | 0.932 | 0.389 | 0 |
| Rps5 | 0 | 1.8679160 | 0.679 | 0.133 | 0 |
| Cux2 | 0 | -4.2456520 | 0.821 | 0.906 | 0 |
| Prdx1 | 0 | 1.0066697 | 0.755 | 0.227 | 0 |
| Plxdc2 | 0 | 1.6362229 | 0.843 | 0.384 | 0 |
| Rps18 | 0 | 1.0258005 | 0.865 | 0.300 | 0 |
| Cfl1 | 0 | 1.2196355 | 0.884 | 0.463 | 0 |
| Man2b1 | 0 | 0.9932871 | 0.886 | 0.399 | 0 |
| Cd52 | 0 | 0.6197818 | 0.738 | 0.187 | 0 |
| Rps6 | 0 | 0.7430137 | 0.779 | 0.197 | 0 |
| Rpl19 | 0 | 1.2497134 | 0.766 | 0.182 | 0 |
| Cox4i1 | 0 | 1.3180256 | 0.795 | 0.227 | 0 |
| Arfgef3 | 0 | -4.0098038 | 0.574 | 0.833 | 0 |
| Rps23-ps1 | 0 | 1.1017877 | 0.841 | 0.246 | 0 |
| Rps16 | 0 | 0.9529365 | 0.817 | 0.246 | 0 |
| Rplp2 | 0 | 0.7315401 | 0.793 | 0.207 | 0 |
| AU020206 | 0 | 2.4513427 | 0.688 | 0.172 | 0 |
| Rps28 | 0 | 1.0094138 | 0.891 | 0.291 | 0 |
| Laptm5 | 0 | 1.2047213 | 0.969 | 0.665 | 0 |
| Rpl3 | 0 | 1.4624131 | 0.773 | 0.232 | 0 |
| Ppt1 | 0 | 1.4212335 | 0.749 | 0.246 | 0 |
| Lamp1 | 0 | 0.4694796 | 0.915 | 0.448 | 0 |
| Creg1 | 0 | 0.9666021 | 0.773 | 0.251 | 0 |
| B2m | 0 | 0.9439195 | 0.989 | 0.734 | 0 |
| Hif1a | 0 | 3.1804196 | 0.587 | 0.074 | 0 |
| Rpl15 | 0 | 0.8104652 | 0.749 | 0.182 | 0 |
| Rpl13 | 0 | 0.7091759 | 0.880 | 0.305 | 0 |
| Rpl35a | 0 | 0.5728594 | 0.736 | 0.172 | 0 |
| Cd83 | 0 | 3.1097143 | 0.629 | 0.128 | 0 |
| Rpl32 | 0 | 0.0061385 | 0.882 | 0.305 | 0 |
| Rbm45 | 0 | -5.0699120 | 0.594 | 0.828 | 0 |
| Hsp90b1 | 0 | 0.6376631 | 0.841 | 0.330 | 0 |
| Pdia3 | 0 | 1.0331859 | 0.828 | 0.325 | 0 |
| Rps8 | 0 | 1.5908680 | 0.714 | 0.187 | 0 |
| Ctss | 0 | 0.9543452 | 1.000 | 0.847 | 0 |
| Ccl3 | 0 | 4.4857741 | 0.533 | 0.044 | 0 |
| Dnajb14 | 0 | 2.3303873 | 0.692 | 0.177 | 0 |
| Cadm1 | 0 | 1.7429086 | 0.651 | 0.143 | 0 |
| Gnas | 0 | 1.7107747 | 0.734 | 0.212 | 0 |
| Rpl10a | 0 | 0.2706754 | 0.801 | 0.261 | 0 |
| Psap | 0 | 0.9238396 | 0.985 | 0.626 | 0 |
| Rpl18 | 0 | 0.7048072 | 0.740 | 0.207 | 0 |
Microglia2_vs_Microglia4
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-52.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Ifit3 | 0 | -6.2941243 | 0.061 | 0.628 | 0.00e+00 |
| Rtp4 | 0 | -2.8837830 | 0.201 | 0.717 | 0.00e+00 |
| Iigp1 | 0 | -5.1929461 | 0.107 | 0.558 | 0.00e+00 |
| Mx1 | 0 | -5.4224647 | 0.096 | 0.522 | 0.00e+00 |
| Ifit3b | 0 | -6.8333059 | 0.096 | 0.504 | 0.00e+00 |
| Ifit2 | 0 | -5.0561604 | 0.055 | 0.425 | 0.00e+00 |
| Stat1 | 0 | -2.5846951 | 0.371 | 0.823 | 0.00e+00 |
| Iigp1c | 0 | -4.3730970 | 0.175 | 0.602 | 0.00e+00 |
| Usp18 | 0 | -4.2910116 | 0.103 | 0.504 | 0.00e+00 |
| Ifi206 | 0 | -5.4664697 | 0.024 | 0.319 | 0.00e+00 |
| Tgtp2 | 0 | -4.2713872 | 0.052 | 0.389 | 0.00e+00 |
| Oasl2 | 0 | -3.4547280 | 0.264 | 0.673 | 0.00e+00 |
| Ccl12 | 0 | -2.8636234 | 0.269 | 0.690 | 0.00e+00 |
| Irf7 | 0 | -3.6899477 | 0.068 | 0.398 | 0.00e+00 |
| Oas2 | 0 | -4.3154382 | 0.037 | 0.327 | 0.00e+00 |
| Ifi209 | 0 | -3.3486548 | 0.111 | 0.469 | 0.00e+00 |
| Lyz2 | 0 | 1.4579243 | 0.921 | 0.708 | 0.00e+00 |
| Rnf213 | 0 | -2.6668510 | 0.229 | 0.628 | 0.00e+00 |
| Trim30a | 0 | -1.8304591 | 0.371 | 0.726 | 0.00e+00 |
| Apoe | 0 | 1.5814612 | 0.937 | 0.726 | 0.00e+00 |
| Clec7a | 0 | 2.2502925 | 0.668 | 0.204 | 0.00e+00 |
| Ifit1 | 0 | -4.7023280 | 0.079 | 0.363 | 0.00e+00 |
| Cst7 | 0 | 2.2102465 | 0.705 | 0.310 | 0.00e+00 |
| Rsad2 | 0 | -6.7067931 | 0.057 | 0.319 | 0.00e+00 |
| Ctsb | 0 | 0.9625566 | 0.993 | 0.965 | 0.00e+00 |
| Ifi211 | 0 | -4.3361877 | 0.039 | 0.283 | 0.00e+00 |
| Ifi204 | 0 | -2.7640857 | 0.417 | 0.726 | 0.00e+00 |
| Oas1g | 0 | -2.8546893 | 0.103 | 0.407 | 0.00e+00 |
| Ifi213 | 0 | -4.5743985 | 0.203 | 0.513 | 0.00e+00 |
| Nlrc5 | 0 | -2.9669339 | 0.118 | 0.425 | 0.00e+00 |
| Herc6 | 0 | -2.9517754 | 0.367 | 0.681 | 0.00e+00 |
| Ftl1 | 0 | 0.9448623 | 0.976 | 0.938 | 0.00e+00 |
| Trex1 | 0 | -1.8325374 | 0.231 | 0.575 | 0.00e+00 |
| Irgm2 | 0 | -2.7177538 | 0.148 | 0.460 | 0.00e+00 |
| Cd63 | 0 | 1.2527303 | 0.893 | 0.664 | 0.00e+00 |
| Phf11a | 0 | -3.7830704 | 0.076 | 0.345 | 0.00e+00 |
| Fcgr1 | 0 | -1.3568162 | 0.596 | 0.850 | 0.00e+00 |
| Helz2 | 0 | -5.0585094 | 0.017 | 0.195 | 0.00e+00 |
| Ifi208 | 0 | -3.8124370 | 0.159 | 0.469 | 0.00e+00 |
| Slfn8 | 0 | -2.6128055 | 0.360 | 0.673 | 0.00e+00 |
| Oas1a | 0 | -2.3506154 | 0.153 | 0.460 | 0.00e+00 |
| Ifitm3 | 0 | -2.2095517 | 0.271 | 0.566 | 0.00e+00 |
| Isg15 | 0 | -3.4470726 | 0.179 | 0.460 | 0.00e+00 |
| Trim30d | 0 | -2.3151606 | 0.255 | 0.584 | 0.00e+00 |
| Ctsd | 0 | 0.8606491 | 1.000 | 0.991 | 0.00e+00 |
| Parp14 | 0 | -3.1715874 | 0.245 | 0.531 | 0.00e+00 |
| Selplg | 0 | -0.8109430 | 0.924 | 0.956 | 0.00e+00 |
| Cd68 | 0 | 1.0343615 | 0.932 | 0.796 | 0.00e+00 |
| Ly6a | 0 | -3.6771203 | 0.024 | 0.204 | 0.00e+00 |
| Mx2 | 0 | -3.0539106 | 0.072 | 0.310 | 0.00e+00 |
| Zbp1 | 0 | -3.1645428 | 0.109 | 0.363 | 0.00e+00 |
| Gapdh | 0 | 1.2064431 | 0.841 | 0.664 | 0.00e+00 |
| Ccl3 | 0 | 2.7723928 | 0.533 | 0.159 | 0.00e+00 |
| Ms4a6b | 0 | -2.1935614 | 0.170 | 0.460 | 0.00e+00 |
| Tyrobp | 0 | 1.1163903 | 0.980 | 0.965 | 1.00e-07 |
| Phf11b | 0 | -2.5719599 | 0.131 | 0.389 | 2.00e-07 |
| Irgm1 | 0 | -2.7120912 | 0.295 | 0.549 | 2.00e-07 |
| Ifi214 | 0 | -3.1527124 | 0.177 | 0.451 | 2.00e-07 |
| Rsrp1 | 0 | -0.9305697 | 0.854 | 0.956 | 2.00e-07 |
| Serinc3 | 0 | -0.6556931 | 0.976 | 1.000 | 3.00e-07 |
| Dhx58 | 0 | -2.3835526 | 0.138 | 0.398 | 3.00e-07 |
| Xaf1 | 0 | -1.8940135 | 0.469 | 0.708 | 3.00e-07 |
| Tmem119 | 0 | -1.0362580 | 0.760 | 0.912 | 4.00e-07 |
| Slfn2 | 0 | -2.5330386 | 0.212 | 0.487 | 4.00e-07 |
| Ctsa | 0 | 0.8417328 | 0.959 | 0.876 | 7.00e-07 |
| Eef1a1 | 0 | 0.6999194 | 0.989 | 0.965 | 9.00e-07 |
| Fgl2 | 0 | -2.5704249 | 0.179 | 0.442 | 1.70e-06 |
| Atp6v0a2 | 0 | -1.2278861 | 0.260 | 0.575 | 2.10e-06 |
| Phf11d | 0 | -2.7701409 | 0.190 | 0.442 | 3.00e-06 |
| P2ry12 | 0 | -0.8110582 | 0.915 | 0.965 | 3.50e-06 |
| Igtp | 0 | -2.4375314 | 0.181 | 0.434 | 3.80e-06 |
| Gbp7 | 0 | -3.8054657 | 0.100 | 0.319 | 4.20e-06 |
| Pmp22 | 0 | 1.4877775 | 0.694 | 0.425 | 4.40e-06 |
| Samd9l | 0 | -2.9468343 | 0.061 | 0.257 | 4.60e-06 |
| Rigi | 0 | -2.8987722 | 0.469 | 0.673 | 4.90e-06 |
| Lpl | 0 | 3.3037468 | 0.825 | 0.708 | 5.20e-06 |
| Dapp1 | 0 | -1.8386634 | 0.271 | 0.540 | 5.80e-06 |
| Tor3a | 0 | -2.0779994 | 0.242 | 0.496 | 7.30e-06 |
| Rpl35rt | 0 | 0.9474910 | 0.915 | 0.779 | 7.60e-06 |
| Sp100 | 0 | -2.1235346 | 0.358 | 0.611 | 8.60e-06 |
| Oasl1 | 0 | -6.1754000 | 0.028 | 0.177 | 8.80e-06 |
| Parp12 | 0 | -2.1341265 | 0.166 | 0.416 | 1.08e-05 |
| Hif1a | 0 | 1.8217006 | 0.587 | 0.274 | 1.08e-05 |
| Ifi207 | 0 | -2.4107599 | 0.120 | 0.354 | 1.23e-05 |
| Ifi205 | 0 | -2.5142149 | 0.022 | 0.159 | 2.19e-05 |
| Ctsz | 0 | 0.6776589 | 0.987 | 0.947 | 2.21e-05 |
| Mif | 0 | 1.5134573 | 0.605 | 0.319 | 2.62e-05 |
| Etnk1 | 0 | -1.7001717 | 0.314 | 0.575 | 2.97e-05 |
| Dtx3l | 0 | -1.5235479 | 0.426 | 0.690 | 3.45e-05 |
| Ifi47 | 0 | -7.4854128 | 0.004 | 0.097 | 4.22e-05 |
| Morc3 | 0 | -1.6687019 | 0.297 | 0.558 | 4.27e-05 |
| Frmd4a | 0 | -0.9326993 | 0.627 | 0.858 | 4.37e-05 |
| Cmpk2 | 0 | -3.7385669 | 0.024 | 0.159 | 4.44e-05 |
| Rpl21 | 0 | 1.0010398 | 0.856 | 0.619 | 5.91e-05 |
| Slfn5 | 0 | -2.7671553 | 0.517 | 0.717 | 5.99e-05 |
| Fth1 | 0 | 0.6611646 | 0.983 | 0.920 | 6.90e-05 |
| Ctsl | 0 | 0.8069538 | 0.969 | 0.938 | 7.08e-05 |
| Syngr1 | 0 | 1.2318438 | 0.810 | 0.611 | 7.43e-05 |
| Gnas | 0 | 1.2406783 | 0.734 | 0.451 | 7.80e-05 |
| Ddx60 | 0 | -2.5908945 | 0.153 | 0.381 | 8.87e-05 |
Microglia2_vs_Microglia4_comorbid
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-55.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Ifit3 | 0 | -6.2941243 | 0.061 | 0.628 | 0.00e+00 |
| Rtp4 | 0 | -2.8837830 | 0.201 | 0.717 | 0.00e+00 |
| Iigp1 | 0 | -5.1929461 | 0.107 | 0.558 | 0.00e+00 |
| Mx1 | 0 | -5.4224647 | 0.096 | 0.522 | 0.00e+00 |
| Ifit3b | 0 | -6.8333059 | 0.096 | 0.504 | 0.00e+00 |
| Ifit2 | 0 | -5.0561604 | 0.055 | 0.425 | 0.00e+00 |
| Stat1 | 0 | -2.5846951 | 0.371 | 0.823 | 0.00e+00 |
| Iigp1c | 0 | -4.3730970 | 0.175 | 0.602 | 0.00e+00 |
| Usp18 | 0 | -4.2910116 | 0.103 | 0.504 | 0.00e+00 |
| Ifi206 | 0 | -5.4664697 | 0.024 | 0.319 | 0.00e+00 |
| Tgtp2 | 0 | -4.2713872 | 0.052 | 0.389 | 0.00e+00 |
| Oasl2 | 0 | -3.4547280 | 0.264 | 0.673 | 0.00e+00 |
| Ccl12 | 0 | -2.8636234 | 0.269 | 0.690 | 0.00e+00 |
| Irf7 | 0 | -3.6899477 | 0.068 | 0.398 | 0.00e+00 |
| Oas2 | 0 | -4.3154382 | 0.037 | 0.327 | 0.00e+00 |
| Ifi209 | 0 | -3.3486548 | 0.111 | 0.469 | 0.00e+00 |
| Lyz2 | 0 | 1.4579243 | 0.921 | 0.708 | 0.00e+00 |
| Rnf213 | 0 | -2.6668510 | 0.229 | 0.628 | 0.00e+00 |
| Trim30a | 0 | -1.8304591 | 0.371 | 0.726 | 0.00e+00 |
| Apoe | 0 | 1.5814612 | 0.937 | 0.726 | 0.00e+00 |
| Clec7a | 0 | 2.2502925 | 0.668 | 0.204 | 0.00e+00 |
| Ifit1 | 0 | -4.7023280 | 0.079 | 0.363 | 0.00e+00 |
| Cst7 | 0 | 2.2102465 | 0.705 | 0.310 | 0.00e+00 |
| Rsad2 | 0 | -6.7067931 | 0.057 | 0.319 | 0.00e+00 |
| Ctsb | 0 | 0.9625566 | 0.993 | 0.965 | 0.00e+00 |
| Ifi211 | 0 | -4.3361877 | 0.039 | 0.283 | 0.00e+00 |
| Ifi204 | 0 | -2.7640857 | 0.417 | 0.726 | 0.00e+00 |
| Oas1g | 0 | -2.8546893 | 0.103 | 0.407 | 0.00e+00 |
| Ifi213 | 0 | -4.5743985 | 0.203 | 0.513 | 0.00e+00 |
| Nlrc5 | 0 | -2.9669339 | 0.118 | 0.425 | 0.00e+00 |
| Herc6 | 0 | -2.9517754 | 0.367 | 0.681 | 0.00e+00 |
| Ftl1 | 0 | 0.9448623 | 0.976 | 0.938 | 0.00e+00 |
| Trex1 | 0 | -1.8325374 | 0.231 | 0.575 | 0.00e+00 |
| Irgm2 | 0 | -2.7177538 | 0.148 | 0.460 | 0.00e+00 |
| Cd63 | 0 | 1.2527303 | 0.893 | 0.664 | 0.00e+00 |
| Phf11a | 0 | -3.7830704 | 0.076 | 0.345 | 0.00e+00 |
| Fcgr1 | 0 | -1.3568162 | 0.596 | 0.850 | 0.00e+00 |
| Helz2 | 0 | -5.0585094 | 0.017 | 0.195 | 0.00e+00 |
| Ifi208 | 0 | -3.8124370 | 0.159 | 0.469 | 0.00e+00 |
| Slfn8 | 0 | -2.6128055 | 0.360 | 0.673 | 0.00e+00 |
| Oas1a | 0 | -2.3506154 | 0.153 | 0.460 | 0.00e+00 |
| Ifitm3 | 0 | -2.2095517 | 0.271 | 0.566 | 0.00e+00 |
| Isg15 | 0 | -3.4470726 | 0.179 | 0.460 | 0.00e+00 |
| Trim30d | 0 | -2.3151606 | 0.255 | 0.584 | 0.00e+00 |
| Ctsd | 0 | 0.8606491 | 1.000 | 0.991 | 0.00e+00 |
| Parp14 | 0 | -3.1715874 | 0.245 | 0.531 | 0.00e+00 |
| Selplg | 0 | -0.8109430 | 0.924 | 0.956 | 0.00e+00 |
| Cd68 | 0 | 1.0343615 | 0.932 | 0.796 | 0.00e+00 |
| Ly6a | 0 | -3.6771203 | 0.024 | 0.204 | 0.00e+00 |
| Mx2 | 0 | -3.0539106 | 0.072 | 0.310 | 0.00e+00 |
| Zbp1 | 0 | -3.1645428 | 0.109 | 0.363 | 0.00e+00 |
| Gapdh | 0 | 1.2064431 | 0.841 | 0.664 | 0.00e+00 |
| Ccl3 | 0 | 2.7723928 | 0.533 | 0.159 | 0.00e+00 |
| Ms4a6b | 0 | -2.1935614 | 0.170 | 0.460 | 0.00e+00 |
| Tyrobp | 0 | 1.1163903 | 0.980 | 0.965 | 1.00e-07 |
| Phf11b | 0 | -2.5719599 | 0.131 | 0.389 | 2.00e-07 |
| Irgm1 | 0 | -2.7120912 | 0.295 | 0.549 | 2.00e-07 |
| Ifi214 | 0 | -3.1527124 | 0.177 | 0.451 | 2.00e-07 |
| Rsrp1 | 0 | -0.9305697 | 0.854 | 0.956 | 2.00e-07 |
| Serinc3 | 0 | -0.6556931 | 0.976 | 1.000 | 3.00e-07 |
| Dhx58 | 0 | -2.3835526 | 0.138 | 0.398 | 3.00e-07 |
| Xaf1 | 0 | -1.8940135 | 0.469 | 0.708 | 3.00e-07 |
| Tmem119 | 0 | -1.0362580 | 0.760 | 0.912 | 4.00e-07 |
| Slfn2 | 0 | -2.5330386 | 0.212 | 0.487 | 4.00e-07 |
| Ctsa | 0 | 0.8417328 | 0.959 | 0.876 | 7.00e-07 |
| Eef1a1 | 0 | 0.6999194 | 0.989 | 0.965 | 9.00e-07 |
| Fgl2 | 0 | -2.5704249 | 0.179 | 0.442 | 1.70e-06 |
| Atp6v0a2 | 0 | -1.2278861 | 0.260 | 0.575 | 2.10e-06 |
| Phf11d | 0 | -2.7701409 | 0.190 | 0.442 | 3.00e-06 |
| P2ry12 | 0 | -0.8110582 | 0.915 | 0.965 | 3.50e-06 |
| Igtp | 0 | -2.4375314 | 0.181 | 0.434 | 3.80e-06 |
| Gbp7 | 0 | -3.8054657 | 0.100 | 0.319 | 4.20e-06 |
| Pmp22 | 0 | 1.4877775 | 0.694 | 0.425 | 4.40e-06 |
| Samd9l | 0 | -2.9468343 | 0.061 | 0.257 | 4.60e-06 |
| Rigi | 0 | -2.8987722 | 0.469 | 0.673 | 4.90e-06 |
| Lpl | 0 | 3.3037468 | 0.825 | 0.708 | 5.20e-06 |
| Dapp1 | 0 | -1.8386634 | 0.271 | 0.540 | 5.80e-06 |
| Tor3a | 0 | -2.0779994 | 0.242 | 0.496 | 7.30e-06 |
| Rpl35rt | 0 | 0.9474910 | 0.915 | 0.779 | 7.60e-06 |
| Sp100 | 0 | -2.1235346 | 0.358 | 0.611 | 8.60e-06 |
| Oasl1 | 0 | -6.1754000 | 0.028 | 0.177 | 8.80e-06 |
| Parp12 | 0 | -2.1341265 | 0.166 | 0.416 | 1.08e-05 |
| Hif1a | 0 | 1.8217006 | 0.587 | 0.274 | 1.08e-05 |
| Ifi207 | 0 | -2.4107599 | 0.120 | 0.354 | 1.23e-05 |
| Ifi205 | 0 | -2.5142149 | 0.022 | 0.159 | 2.19e-05 |
| Ctsz | 0 | 0.6776589 | 0.987 | 0.947 | 2.21e-05 |
| Mif | 0 | 1.5134573 | 0.605 | 0.319 | 2.62e-05 |
| Etnk1 | 0 | -1.7001717 | 0.314 | 0.575 | 2.97e-05 |
| Dtx3l | 0 | -1.5235479 | 0.426 | 0.690 | 3.45e-05 |
| Ifi47 | 0 | -7.4854128 | 0.004 | 0.097 | 4.22e-05 |
| Morc3 | 0 | -1.6687019 | 0.297 | 0.558 | 4.27e-05 |
| Frmd4a | 0 | -0.9326993 | 0.627 | 0.858 | 4.37e-05 |
| Cmpk2 | 0 | -3.7385669 | 0.024 | 0.159 | 4.44e-05 |
| Rpl21 | 0 | 1.0010398 | 0.856 | 0.619 | 5.91e-05 |
| Slfn5 | 0 | -2.7671553 | 0.517 | 0.717 | 5.99e-05 |
| Fth1 | 0 | 0.6611646 | 0.983 | 0.920 | 6.90e-05 |
| Ctsl | 0 | 0.8069538 | 0.969 | 0.938 | 7.08e-05 |
| Syngr1 | 0 | 1.2318438 | 0.810 | 0.611 | 7.43e-05 |
| Gnas | 0 | 1.2406783 | 0.734 | 0.451 | 7.80e-05 |
| Ddx60 | 0 | -2.5908945 | 0.153 | 0.381 | 8.87e-05 |
Microglia2_vs_Microglia5
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-58.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| H2-Ab1 | 0.0000000 | -5.3451229 | 0.144 | 0.904 | 0.0000000 |
| H2-Eb1 | 0.0000000 | -7.1667700 | 0.031 | 0.630 | 0.0000000 |
| H2-Aa | 0.0000000 | -6.2384326 | 0.109 | 0.712 | 0.0000000 |
| Cd74 | 0.0000000 | -4.7767701 | 0.443 | 0.959 | 0.0000000 |
| Apoe | 0.0000000 | 2.4085403 | 0.937 | 0.753 | 0.0000000 |
| Selplg | 0.0000000 | -1.0407621 | 0.924 | 0.986 | 0.0000002 |
| Cd63 | 0.0000000 | 1.2786389 | 0.893 | 0.685 | 0.0000008 |
| H2-D1 | 0.0000000 | -0.9645578 | 0.941 | 0.959 | 0.0000048 |
| Rpl35rt | 0.0000000 | 1.2894276 | 0.915 | 0.685 | 0.0000089 |
| Lyz2 | 0.0000000 | 1.0563367 | 0.921 | 0.685 | 0.0000115 |
| P2ry12 | 0.0000000 | -1.1235935 | 0.915 | 0.959 | 0.0000160 |
| Tmem119 | 0.0000000 | -1.2422070 | 0.760 | 0.877 | 0.0001208 |
| Ftl1 | 0.0000000 | 0.7586969 | 0.976 | 0.973 | 0.0003264 |
| Lpl | 0.0000000 | 2.5225444 | 0.825 | 0.616 | 0.0007345 |
| Hoxb1 | 0.0000001 | -0.9117428 | 0.105 | 0.342 | 0.0011121 |
| Fth1 | 0.0000001 | 0.7333233 | 0.983 | 1.000 | 0.0016283 |
| Ctsz | 0.0000001 | 0.6747200 | 0.987 | 0.890 | 0.0017341 |
| Clec7a | 0.0000001 | 1.1260543 | 0.668 | 0.288 | 0.0020302 |
| Gnas | 0.0000002 | 1.3946833 | 0.734 | 0.438 | 0.0027413 |
| Cst7 | 0.0000002 | 1.0062695 | 0.705 | 0.301 | 0.0030008 |
| Csf1r | 0.0000002 | -0.5243534 | 0.991 | 1.000 | 0.0036012 |
| Irgm2 | 0.0000004 | -2.0859889 | 0.148 | 0.384 | 0.0058809 |
| Ccl3 | 0.0000005 | 2.9802710 | 0.533 | 0.260 | 0.0079733 |
| Jcad | 0.0000005 | -4.8386824 | 0.000 | 0.055 | 0.0081954 |
| Mt1 | 0.0000008 | 1.1930677 | 0.594 | 0.288 | 0.0124939 |
| Ftl1-ps1 | 0.0000008 | 1.5767103 | 0.779 | 0.562 | 0.0129632 |
| Hrh2 | 0.0000012 | -4.7767855 | 0.033 | 0.164 | 0.0184060 |
| Rpl21 | 0.0000013 | 0.9058642 | 0.856 | 0.630 | 0.0202140 |
| Rpl7 | 0.0000019 | 1.0947626 | 0.930 | 0.822 | 0.0308589 |
| Ccl4 | 0.0000023 | 3.1030600 | 0.332 | 0.055 | 0.0362273 |
| Hif1a | 0.0000027 | 1.4173114 | 0.587 | 0.274 | 0.0428335 |
| Tpst2 | 0.0000030 | -1.8131180 | 0.273 | 0.493 | 0.0477700 |
| Ctsb | 0.0000036 | 0.5891559 | 0.993 | 0.959 | 0.0573673 |
| Pfkm | 0.0000038 | -2.5260504 | 0.007 | 0.082 | 0.0607689 |
| Tpt1 | 0.0000053 | 0.8034978 | 0.825 | 0.589 | 0.0846516 |
| Upk1b | 0.0000066 | -2.1526737 | 0.094 | 0.274 | 0.1044726 |
| Rpl13a | 0.0000068 | 0.6557451 | 0.917 | 0.808 | 0.1090125 |
| Zfp109 | 0.0000086 | -3.1435187 | 0.004 | 0.068 | 0.1364508 |
| H2-K1 | 0.0000111 | -0.7444660 | 0.900 | 0.932 | 0.1765875 |
| Siglech | 0.0000115 | -0.8672070 | 0.882 | 0.945 | 0.1826192 |
| Rpl35 | 0.0000148 | 0.9585920 | 0.928 | 0.753 | 0.2367280 |
| Mmp28 | 0.0000166 | -1.9845774 | 0.002 | 0.055 | 0.2648944 |
| Tnc | 0.0000166 | -2.3775443 | 0.002 | 0.055 | 0.2648944 |
| Cd68 | 0.0000178 | 0.6524691 | 0.932 | 0.877 | 0.2836960 |
| Rplp1 | 0.0000188 | 0.6910374 | 0.932 | 0.822 | 0.2994568 |
| Rps25 | 0.0000200 | 0.7754654 | 0.865 | 0.753 | 0.3189262 |
| Ciita | 0.0000216 | -4.8095763 | 0.028 | 0.137 | 0.3442854 |
| P2ry13 | 0.0000223 | -0.9586586 | 0.701 | 0.849 | 0.3549733 |
| Lilrb4a | 0.0000230 | 2.6716423 | 0.345 | 0.110 | 0.3665061 |
| Fgd2 | 0.0000268 | -1.2655078 | 0.522 | 0.685 | 0.4278358 |
| C3ar1 | 0.0000271 | 1.0458375 | 0.664 | 0.438 | 0.4314617 |
| H2-Oa | 0.0000290 | -1.7206777 | 0.162 | 0.356 | 0.4616728 |
| Rps9 | 0.0000296 | 0.6099635 | 0.884 | 0.753 | 0.4723822 |
| Susd3 | 0.0000300 | -1.2473605 | 0.500 | 0.658 | 0.4783200 |
| Rps26 | 0.0000309 | 0.6608937 | 0.742 | 0.479 | 0.4921130 |
| Ctsd | 0.0000318 | 0.4789682 | 1.000 | 0.973 | 0.5078206 |
| Eif4a1 | 0.0000320 | 1.0686170 | 0.769 | 0.562 | 0.5103260 |
| Rpl41 | 0.0000346 | 0.6099427 | 0.930 | 0.795 | 0.5520143 |
| Rpl18a | 0.0000371 | 0.4685572 | 0.952 | 0.863 | 0.5912313 |
| Gusb | 0.0000423 | 1.0873203 | 0.793 | 0.644 | 0.6743211 |
| Il17ra | 0.0000443 | -1.9969095 | 0.293 | 0.493 | 0.7059775 |
| Cmtm7 | 0.0000472 | -1.2546507 | 0.439 | 0.644 | 0.7530573 |
| Apbb2 | 0.0000525 | 1.6106863 | 0.459 | 0.205 | 0.8374611 |
| Rpl7a | 0.0000636 | 0.7322386 | 0.699 | 0.466 | 1.0000000 |
| Ndufb2 | 0.0000656 | 2.5001517 | 0.504 | 0.315 | 1.0000000 |
| Rps28 | 0.0000672 | 0.7057895 | 0.891 | 0.808 | 1.0000000 |
| Rnase6 | 0.0000707 | -1.3677990 | 0.068 | 0.205 | 1.0000000 |
| Rpl18 | 0.0000709 | 0.8570031 | 0.740 | 0.479 | 1.0000000 |
| Cx3cr1 | 0.0000844 | -0.5724904 | 0.972 | 0.945 | 1.0000000 |
| Adamts6 | 0.0000859 | -0.8170736 | 0.026 | 0.123 | 1.0000000 |
| Prkca | 0.0000873 | -2.1854205 | 0.105 | 0.260 | 1.0000000 |
| Mir8114 | 0.0000896 | -1.8108627 | 0.186 | 0.384 | 1.0000000 |
| Tpd52 | 0.0000897 | 1.0237119 | 0.633 | 0.397 | 1.0000000 |
| Pld4 | 0.0000902 | -0.7632094 | 0.803 | 0.904 | 1.0000000 |
| Cmtm6 | 0.0000934 | -1.1980312 | 0.592 | 0.767 | 1.0000000 |
| Cd9 | 0.0000954 | 0.5419159 | 0.969 | 0.945 | 1.0000000 |
| Smim29 | 0.0001133 | 1.7796118 | 0.334 | 0.110 | 1.0000000 |
| Glul | 0.0001292 | -0.8817242 | 0.655 | 0.808 | 1.0000000 |
| Rnase4 | 0.0001348 | -0.5705109 | 0.797 | 0.932 | 1.0000000 |
| Rpl37a | 0.0001369 | 0.5922122 | 0.865 | 0.726 | 1.0000000 |
| Uba52rt | 0.0001420 | 0.7456597 | 0.755 | 0.589 | 1.0000000 |
| Myo1e | 0.0001421 | 1.7887827 | 0.358 | 0.137 | 1.0000000 |
| Plaur | 0.0001527 | 2.4814429 | 0.290 | 0.082 | 1.0000000 |
| Ltb | 0.0001541 | -3.9409280 | 0.004 | 0.055 | 1.0000000 |
| Uba52 | 0.0001550 | 0.6482223 | 0.812 | 0.589 | 1.0000000 |
| Cd81 | 0.0001556 | -0.3331951 | 0.991 | 1.000 | 1.0000000 |
| Colec10 | 0.0001626 | -3.5311507 | 0.004 | 0.055 | 1.0000000 |
| Dcst1 | 0.0001668 | -2.1432968 | 0.146 | 0.315 | 1.0000000 |
| Or5v1b | 0.0001706 | 0.4972863 | 0.247 | 0.041 | 1.0000000 |
| Malat1 | 0.0001733 | -0.2811189 | 0.952 | 0.973 | 1.0000000 |
| H2-Q7 | 0.0001774 | -2.1227370 | 0.454 | 0.603 | 1.0000000 |
| Dnajc12 | 0.0001815 | -0.7394357 | 0.308 | 0.534 | 1.0000000 |
| Serf2 | 0.0001857 | 0.8133924 | 0.784 | 0.575 | 1.0000000 |
| Rps12l1 | 0.0001875 | 1.4113647 | 0.629 | 0.425 | 1.0000000 |
| Sesn1 | 0.0002018 | -1.7074962 | 0.225 | 0.411 | 1.0000000 |
| Axl | 0.0002025 | 1.1336636 | 0.533 | 0.301 | 1.0000000 |
| Slc13a3 | 0.0002125 | -3.3341157 | 0.024 | 0.110 | 1.0000000 |
| Rpl3 | 0.0002196 | 0.8025449 | 0.773 | 0.603 | 1.0000000 |
| Rplp0 | 0.0002304 | 0.7392331 | 0.852 | 0.712 | 1.0000000 |
| Cd63-ps | 0.0002323 | 0.6916063 | 0.328 | 0.110 | 1.0000000 |
Microglia2_vs_Microglia5_comorbid
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-61.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| H2-Ab1 | 0.0000000 | -5.3451229 | 0.144 | 0.904 | 0.0000000 |
| H2-Eb1 | 0.0000000 | -7.1667700 | 0.031 | 0.630 | 0.0000000 |
| H2-Aa | 0.0000000 | -6.2384326 | 0.109 | 0.712 | 0.0000000 |
| Cd74 | 0.0000000 | -4.7767701 | 0.443 | 0.959 | 0.0000000 |
| Apoe | 0.0000000 | 2.4085403 | 0.937 | 0.753 | 0.0000000 |
| Selplg | 0.0000000 | -1.0407621 | 0.924 | 0.986 | 0.0000002 |
| Cd63 | 0.0000000 | 1.2786389 | 0.893 | 0.685 | 0.0000008 |
| H2-D1 | 0.0000000 | -0.9645578 | 0.941 | 0.959 | 0.0000048 |
| Rpl35rt | 0.0000000 | 1.2894276 | 0.915 | 0.685 | 0.0000089 |
| Lyz2 | 0.0000000 | 1.0563367 | 0.921 | 0.685 | 0.0000115 |
| P2ry12 | 0.0000000 | -1.1235935 | 0.915 | 0.959 | 0.0000160 |
| Tmem119 | 0.0000000 | -1.2422070 | 0.760 | 0.877 | 0.0001208 |
| Ftl1 | 0.0000000 | 0.7586969 | 0.976 | 0.973 | 0.0003264 |
| Lpl | 0.0000000 | 2.5225444 | 0.825 | 0.616 | 0.0007345 |
| Hoxb1 | 0.0000001 | -0.9117428 | 0.105 | 0.342 | 0.0011121 |
| Fth1 | 0.0000001 | 0.7333233 | 0.983 | 1.000 | 0.0016283 |
| Ctsz | 0.0000001 | 0.6747200 | 0.987 | 0.890 | 0.0017341 |
| Clec7a | 0.0000001 | 1.1260543 | 0.668 | 0.288 | 0.0020302 |
| Gnas | 0.0000002 | 1.3946833 | 0.734 | 0.438 | 0.0027413 |
| Cst7 | 0.0000002 | 1.0062695 | 0.705 | 0.301 | 0.0030008 |
| Csf1r | 0.0000002 | -0.5243534 | 0.991 | 1.000 | 0.0036012 |
| Irgm2 | 0.0000004 | -2.0859889 | 0.148 | 0.384 | 0.0058809 |
| Ccl3 | 0.0000005 | 2.9802710 | 0.533 | 0.260 | 0.0079733 |
| Jcad | 0.0000005 | -4.8386824 | 0.000 | 0.055 | 0.0081954 |
| Mt1 | 0.0000008 | 1.1930677 | 0.594 | 0.288 | 0.0124939 |
| Ftl1-ps1 | 0.0000008 | 1.5767103 | 0.779 | 0.562 | 0.0129632 |
| Hrh2 | 0.0000012 | -4.7767855 | 0.033 | 0.164 | 0.0184060 |
| Rpl21 | 0.0000013 | 0.9058642 | 0.856 | 0.630 | 0.0202140 |
| Rpl7 | 0.0000019 | 1.0947626 | 0.930 | 0.822 | 0.0308589 |
| Ccl4 | 0.0000023 | 3.1030600 | 0.332 | 0.055 | 0.0362273 |
| Hif1a | 0.0000027 | 1.4173114 | 0.587 | 0.274 | 0.0428335 |
| Tpst2 | 0.0000030 | -1.8131180 | 0.273 | 0.493 | 0.0477700 |
| Ctsb | 0.0000036 | 0.5891559 | 0.993 | 0.959 | 0.0573673 |
| Pfkm | 0.0000038 | -2.5260504 | 0.007 | 0.082 | 0.0607689 |
| Tpt1 | 0.0000053 | 0.8034978 | 0.825 | 0.589 | 0.0846516 |
| Upk1b | 0.0000066 | -2.1526737 | 0.094 | 0.274 | 0.1044726 |
| Rpl13a | 0.0000068 | 0.6557451 | 0.917 | 0.808 | 0.1090125 |
| Zfp109 | 0.0000086 | -3.1435187 | 0.004 | 0.068 | 0.1364508 |
| H2-K1 | 0.0000111 | -0.7444660 | 0.900 | 0.932 | 0.1765875 |
| Siglech | 0.0000115 | -0.8672070 | 0.882 | 0.945 | 0.1826192 |
| Rpl35 | 0.0000148 | 0.9585920 | 0.928 | 0.753 | 0.2367280 |
| Mmp28 | 0.0000166 | -1.9845774 | 0.002 | 0.055 | 0.2648944 |
| Tnc | 0.0000166 | -2.3775443 | 0.002 | 0.055 | 0.2648944 |
| Cd68 | 0.0000178 | 0.6524691 | 0.932 | 0.877 | 0.2836960 |
| Rplp1 | 0.0000188 | 0.6910374 | 0.932 | 0.822 | 0.2994568 |
| Rps25 | 0.0000200 | 0.7754654 | 0.865 | 0.753 | 0.3189262 |
| Ciita | 0.0000216 | -4.8095763 | 0.028 | 0.137 | 0.3442854 |
| P2ry13 | 0.0000223 | -0.9586586 | 0.701 | 0.849 | 0.3549733 |
| Lilrb4a | 0.0000230 | 2.6716423 | 0.345 | 0.110 | 0.3665061 |
| Fgd2 | 0.0000268 | -1.2655078 | 0.522 | 0.685 | 0.4278358 |
| C3ar1 | 0.0000271 | 1.0458375 | 0.664 | 0.438 | 0.4314617 |
| H2-Oa | 0.0000290 | -1.7206777 | 0.162 | 0.356 | 0.4616728 |
| Rps9 | 0.0000296 | 0.6099635 | 0.884 | 0.753 | 0.4723822 |
| Susd3 | 0.0000300 | -1.2473605 | 0.500 | 0.658 | 0.4783200 |
| Rps26 | 0.0000309 | 0.6608937 | 0.742 | 0.479 | 0.4921130 |
| Ctsd | 0.0000318 | 0.4789682 | 1.000 | 0.973 | 0.5078206 |
| Eif4a1 | 0.0000320 | 1.0686170 | 0.769 | 0.562 | 0.5103260 |
| Rpl41 | 0.0000346 | 0.6099427 | 0.930 | 0.795 | 0.5520143 |
| Rpl18a | 0.0000371 | 0.4685572 | 0.952 | 0.863 | 0.5912313 |
| Gusb | 0.0000423 | 1.0873203 | 0.793 | 0.644 | 0.6743211 |
| Il17ra | 0.0000443 | -1.9969095 | 0.293 | 0.493 | 0.7059775 |
| Cmtm7 | 0.0000472 | -1.2546507 | 0.439 | 0.644 | 0.7530573 |
| Apbb2 | 0.0000525 | 1.6106863 | 0.459 | 0.205 | 0.8374611 |
| Rpl7a | 0.0000636 | 0.7322386 | 0.699 | 0.466 | 1.0000000 |
| Ndufb2 | 0.0000656 | 2.5001517 | 0.504 | 0.315 | 1.0000000 |
| Rps28 | 0.0000672 | 0.7057895 | 0.891 | 0.808 | 1.0000000 |
| Rnase6 | 0.0000707 | -1.3677990 | 0.068 | 0.205 | 1.0000000 |
| Rpl18 | 0.0000709 | 0.8570031 | 0.740 | 0.479 | 1.0000000 |
| Cx3cr1 | 0.0000844 | -0.5724904 | 0.972 | 0.945 | 1.0000000 |
| Adamts6 | 0.0000859 | -0.8170736 | 0.026 | 0.123 | 1.0000000 |
| Prkca | 0.0000873 | -2.1854205 | 0.105 | 0.260 | 1.0000000 |
| Mir8114 | 0.0000896 | -1.8108627 | 0.186 | 0.384 | 1.0000000 |
| Tpd52 | 0.0000897 | 1.0237119 | 0.633 | 0.397 | 1.0000000 |
| Pld4 | 0.0000902 | -0.7632094 | 0.803 | 0.904 | 1.0000000 |
| Cmtm6 | 0.0000934 | -1.1980312 | 0.592 | 0.767 | 1.0000000 |
| Cd9 | 0.0000954 | 0.5419159 | 0.969 | 0.945 | 1.0000000 |
| Smim29 | 0.0001133 | 1.7796118 | 0.334 | 0.110 | 1.0000000 |
| Glul | 0.0001292 | -0.8817242 | 0.655 | 0.808 | 1.0000000 |
| Rnase4 | 0.0001348 | -0.5705109 | 0.797 | 0.932 | 1.0000000 |
| Rpl37a | 0.0001369 | 0.5922122 | 0.865 | 0.726 | 1.0000000 |
| Uba52rt | 0.0001420 | 0.7456597 | 0.755 | 0.589 | 1.0000000 |
| Myo1e | 0.0001421 | 1.7887827 | 0.358 | 0.137 | 1.0000000 |
| Plaur | 0.0001527 | 2.4814429 | 0.290 | 0.082 | 1.0000000 |
| Ltb | 0.0001541 | -3.9409280 | 0.004 | 0.055 | 1.0000000 |
| Uba52 | 0.0001550 | 0.6482223 | 0.812 | 0.589 | 1.0000000 |
| Cd81 | 0.0001556 | -0.3331951 | 0.991 | 1.000 | 1.0000000 |
| Colec10 | 0.0001626 | -3.5311507 | 0.004 | 0.055 | 1.0000000 |
| Dcst1 | 0.0001668 | -2.1432968 | 0.146 | 0.315 | 1.0000000 |
| Or5v1b | 0.0001706 | 0.4972863 | 0.247 | 0.041 | 1.0000000 |
| Malat1 | 0.0001733 | -0.2811189 | 0.952 | 0.973 | 1.0000000 |
| H2-Q7 | 0.0001774 | -2.1227370 | 0.454 | 0.603 | 1.0000000 |
| Dnajc12 | 0.0001815 | -0.7394357 | 0.308 | 0.534 | 1.0000000 |
| Serf2 | 0.0001857 | 0.8133924 | 0.784 | 0.575 | 1.0000000 |
| Rps12l1 | 0.0001875 | 1.4113647 | 0.629 | 0.425 | 1.0000000 |
| Sesn1 | 0.0002018 | -1.7074962 | 0.225 | 0.411 | 1.0000000 |
| Axl | 0.0002025 | 1.1336636 | 0.533 | 0.301 | 1.0000000 |
| Slc13a3 | 0.0002125 | -3.3341157 | 0.024 | 0.110 | 1.0000000 |
| Rpl3 | 0.0002196 | 0.8025449 | 0.773 | 0.603 | 1.0000000 |
| Rplp0 | 0.0002304 | 0.7392331 | 0.852 | 0.712 | 1.0000000 |
| Cd63-ps | 0.0002323 | 0.6916063 | 0.328 | 0.110 | 1.0000000 |
Microglia3_vs_Microglia4
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-64.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Stat1 | 0 | -3.8715741 | 0.108 | 0.823 | 0 |
| Ccl12 | 0 | -5.8058951 | 0.034 | 0.690 | 0 |
| Oasl2 | 0 | -8.9701768 | 0.034 | 0.673 | 0 |
| Rtp4 | 0 | -4.4318702 | 0.059 | 0.717 | 0 |
| Ifit3 | 0 | -10.2130141 | 0.020 | 0.628 | 0 |
| Lgals3bp | 0 | -3.7784573 | 0.158 | 0.814 | 0 |
| Ifi204 | 0 | -2.5040501 | 0.113 | 0.726 | 0 |
| Fcgr1 | 0 | -1.6497400 | 0.232 | 0.850 | 0 |
| H2-D1 | 0 | -2.4643210 | 0.355 | 0.903 | 0 |
| Ifi27l2a | 0 | -3.9338241 | 0.020 | 0.540 | 0 |
| Rnf213 | 0 | -3.7592791 | 0.074 | 0.628 | 0 |
| Trim30a | 0 | -0.3563569 | 0.128 | 0.726 | 0 |
| Iigp1c | 0 | -3.7352198 | 0.079 | 0.602 | 0 |
| Usp18 | 0 | -5.8754808 | 0.020 | 0.504 | 0 |
| Ifit3b | 0 | -6.8947569 | 0.025 | 0.504 | 0 |
| Psmb8 | 0 | -2.0280511 | 0.108 | 0.690 | 0 |
| Rab3gap1 | 0 | -1.7515800 | 0.207 | 0.823 | 0 |
| Ly6e | 0 | -2.0375461 | 0.404 | 0.912 | 0 |
| Ifitm3 | 0 | -2.5258656 | 0.074 | 0.566 | 0 |
| Trim30d | 0 | -3.0262847 | 0.074 | 0.584 | 0 |
| Mx1 | 0 | -6.4073074 | 0.054 | 0.522 | 0 |
| Iigp1 | 0 | -4.8726788 | 0.069 | 0.558 | 0 |
| Trex1 | 0 | -4.0118002 | 0.089 | 0.575 | 0 |
| Dtx3l | 0 | -0.8063297 | 0.148 | 0.690 | 0 |
| Bst2 | 0 | -3.5302365 | 0.069 | 0.558 | 0 |
| Znfx1 | 0 | -4.4684102 | 0.054 | 0.522 | 0 |
| Rigi | 0 | -5.6755913 | 0.177 | 0.673 | 0 |
| Oas1a | 0 | -4.4667086 | 0.020 | 0.460 | 0 |
| Ifi209 | 0 | -5.4750466 | 0.030 | 0.469 | 0 |
| Gvin1 | 0 | -3.4926248 | 0.089 | 0.593 | 0 |
| Slfn2 | 0 | -3.2134389 | 0.034 | 0.487 | 0 |
| H2-T23 | 0 | -2.7101540 | 0.281 | 0.779 | 0 |
| Gvin2 | 0 | -2.6178202 | 0.094 | 0.593 | 0 |
| Frmd4a | 0 | -0.7291505 | 0.286 | 0.858 | 0 |
| Ifit2 | 0 | -6.6922227 | 0.015 | 0.425 | 0 |
| Gvin-ps7 | 0 | -3.5887785 | 0.079 | 0.558 | 0 |
| Ifi213 | 0 | -4.2683077 | 0.064 | 0.513 | 0 |
| H2-K1 | 0 | -1.9933750 | 0.389 | 0.841 | 0 |
| Ctsd | 0 | -1.4319144 | 0.793 | 0.991 | 0 |
| Xaf1 | 0 | -2.1698091 | 0.202 | 0.708 | 0 |
| Sp110 | 0 | -4.2252854 | 0.059 | 0.513 | 0 |
| Tgtp2 | 0 | -9.5850755 | 0.005 | 0.389 | 0 |
| Fgl2 | 0 | -4.6728295 | 0.025 | 0.442 | 0 |
| Irgm1 | 0 | -3.3847754 | 0.084 | 0.549 | 0 |
| Slc38a6 | 0 | -0.7939891 | 0.369 | 0.894 | 0 |
| Ctsz | 0 | -1.3676100 | 0.552 | 0.947 | 0 |
| Nlrc5 | 0 | -5.0470359 | 0.020 | 0.425 | 0 |
| Ppp2r5a | 0 | -1.2606889 | 0.182 | 0.743 | 0 |
| AU020206 | 0 | -2.2173204 | 0.172 | 0.690 | 0 |
| Samhd1 | 0 | -1.1072513 | 0.177 | 0.717 | 0 |
| Psap | 0 | -1.2073459 | 0.626 | 0.973 | 0 |
| Serpine2 | 0 | -1.6291886 | 0.369 | 0.876 | 0 |
| Ctsh | 0 | -0.1872340 | 0.379 | 0.885 | 0 |
| Serf2 | 0 | -0.9470411 | 0.182 | 0.752 | 0 |
| Grn | 0 | -1.2197911 | 0.473 | 0.938 | 0 |
| Irf7 | 0 | -7.5365346 | 0.015 | 0.398 | 0 |
| Scamp2 | 0 | -0.8571562 | 0.296 | 0.796 | 0 |
| Rsrp1 | 0 | -1.0764042 | 0.468 | 0.956 | 0 |
| Parp14 | 0 | -5.8054336 | 0.099 | 0.531 | 0 |
| Slfn8 | 0 | -1.3030567 | 0.167 | 0.673 | 0 |
| Ctsb | 0 | -1.1516067 | 0.586 | 0.965 | 0 |
| Tmcc3 | 0 | -1.4966226 | 0.118 | 0.628 | 0 |
| Oas1g | 0 | -4.0795742 | 0.020 | 0.407 | 0 |
| Hexa | 0 | -0.9593763 | 0.409 | 0.894 | 0 |
| Hsp90b1 | 0 | -0.4787846 | 0.330 | 0.858 | 0 |
| C1qa | 0 | -1.2082081 | 0.675 | 1.000 | 0 |
| Zfp488 | 0 | -1.5944163 | 0.192 | 0.752 | 0 |
| C1qc | 0 | -1.1968656 | 0.729 | 0.991 | 0 |
| Hmmr | 0 | -1.7717395 | 0.094 | 0.558 | 0 |
| Ncl | 0 | -1.4222573 | 0.236 | 0.752 | 0 |
| Psme1 | 0 | -2.0139909 | 0.099 | 0.540 | 0 |
| Laptm5 | 0 | -1.2177837 | 0.665 | 0.965 | 0 |
| Ifi207 | 0 | -8.7601559 | 0.005 | 0.354 | 0 |
| Cd9 | 0 | -1.4140766 | 0.537 | 0.938 | 0 |
| Ifi208 | 0 | -4.3919174 | 0.054 | 0.469 | 0 |
| Isg15 | 0 | -4.2016957 | 0.054 | 0.460 | 0 |
| Sgk3 | 0 | -1.5027511 | 0.138 | 0.646 | 0 |
| Man2b1 | 0 | -0.9043467 | 0.399 | 0.885 | 0 |
| Dcbld2 | 0 | 0.1416245 | 0.227 | 0.761 | 0 |
| Rpl18a | 0 | -0.6125305 | 0.389 | 0.947 | 0 |
| Sema4d | 0 | -1.7259783 | 0.187 | 0.681 | 0 |
| Csf3r | 0 | -1.7711726 | 0.330 | 0.814 | 0 |
| Parp9 | 0 | -4.0149973 | 0.020 | 0.389 | 0 |
| Pikfyve | 0 | -0.5615008 | 0.296 | 0.858 | 0 |
| Tmbim6 | 0 | -1.4821522 | 0.365 | 0.841 | 0 |
| Ncf2 | 0 | -0.1795121 | 0.222 | 0.735 | 0 |
| Pdia3 | 0 | -1.0344954 | 0.325 | 0.823 | 0 |
| Herc6 | 0 | -1.4670957 | 0.207 | 0.681 | 0 |
| Atf2 | 0 | -1.2207374 | 0.113 | 0.558 | 0 |
| Ifi214 | 0 | -3.9696484 | 0.049 | 0.451 | 0 |
| Stat2 | 0 | -2.8637168 | 0.158 | 0.619 | 0 |
| Slfn9 | 0 | -2.6545765 | 0.167 | 0.681 | 0 |
| Eif2ak2 | 0 | -0.8729874 | 0.286 | 0.779 | 0 |
| Unc93b1 | 0 | -0.6736716 | 0.365 | 0.894 | 0 |
| Lag3 | 0 | -1.3185418 | 0.340 | 0.814 | 0 |
| Tmem234 | 0 | -2.0836862 | 0.212 | 0.717 | 0 |
| Zbp1 | 0 | -6.5769951 | 0.015 | 0.363 | 0 |
| Acot4 | 0 | 0.4015670 | 0.158 | 0.611 | 0 |
| Fcgr2b | 0 | -0.5420644 | 0.300 | 0.867 | 0 |
| Sfi1 | 0 | -1.9027834 | 0.291 | 0.779 | 0 |
Microglia3_vs_Microglia4_comorbid
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-67.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Stat1 | 0 | -3.8715741 | 0.108 | 0.823 | 0 |
| Ccl12 | 0 | -5.8058951 | 0.034 | 0.690 | 0 |
| Oasl2 | 0 | -8.9701768 | 0.034 | 0.673 | 0 |
| Rtp4 | 0 | -4.4318702 | 0.059 | 0.717 | 0 |
| Ifit3 | 0 | -10.2130141 | 0.020 | 0.628 | 0 |
| Lgals3bp | 0 | -3.7784573 | 0.158 | 0.814 | 0 |
| Ifi204 | 0 | -2.5040501 | 0.113 | 0.726 | 0 |
| Fcgr1 | 0 | -1.6497400 | 0.232 | 0.850 | 0 |
| H2-D1 | 0 | -2.4643210 | 0.355 | 0.903 | 0 |
| Ifi27l2a | 0 | -3.9338241 | 0.020 | 0.540 | 0 |
| Rnf213 | 0 | -3.7592791 | 0.074 | 0.628 | 0 |
| Trim30a | 0 | -0.3563569 | 0.128 | 0.726 | 0 |
| Iigp1c | 0 | -3.7352198 | 0.079 | 0.602 | 0 |
| Usp18 | 0 | -5.8754808 | 0.020 | 0.504 | 0 |
| Ifit3b | 0 | -6.8947569 | 0.025 | 0.504 | 0 |
| Psmb8 | 0 | -2.0280511 | 0.108 | 0.690 | 0 |
| Rab3gap1 | 0 | -1.7515800 | 0.207 | 0.823 | 0 |
| Ly6e | 0 | -2.0375461 | 0.404 | 0.912 | 0 |
| Ifitm3 | 0 | -2.5258656 | 0.074 | 0.566 | 0 |
| Trim30d | 0 | -3.0262847 | 0.074 | 0.584 | 0 |
| Mx1 | 0 | -6.4073074 | 0.054 | 0.522 | 0 |
| Iigp1 | 0 | -4.8726788 | 0.069 | 0.558 | 0 |
| Trex1 | 0 | -4.0118002 | 0.089 | 0.575 | 0 |
| Dtx3l | 0 | -0.8063297 | 0.148 | 0.690 | 0 |
| Bst2 | 0 | -3.5302365 | 0.069 | 0.558 | 0 |
| Znfx1 | 0 | -4.4684102 | 0.054 | 0.522 | 0 |
| Rigi | 0 | -5.6755913 | 0.177 | 0.673 | 0 |
| Oas1a | 0 | -4.4667086 | 0.020 | 0.460 | 0 |
| Ifi209 | 0 | -5.4750466 | 0.030 | 0.469 | 0 |
| Gvin1 | 0 | -3.4926248 | 0.089 | 0.593 | 0 |
| Slfn2 | 0 | -3.2134389 | 0.034 | 0.487 | 0 |
| H2-T23 | 0 | -2.7101540 | 0.281 | 0.779 | 0 |
| Gvin2 | 0 | -2.6178202 | 0.094 | 0.593 | 0 |
| Frmd4a | 0 | -0.7291505 | 0.286 | 0.858 | 0 |
| Ifit2 | 0 | -6.6922227 | 0.015 | 0.425 | 0 |
| Gvin-ps7 | 0 | -3.5887785 | 0.079 | 0.558 | 0 |
| Ifi213 | 0 | -4.2683077 | 0.064 | 0.513 | 0 |
| H2-K1 | 0 | -1.9933750 | 0.389 | 0.841 | 0 |
| Ctsd | 0 | -1.4319144 | 0.793 | 0.991 | 0 |
| Xaf1 | 0 | -2.1698091 | 0.202 | 0.708 | 0 |
| Sp110 | 0 | -4.2252854 | 0.059 | 0.513 | 0 |
| Tgtp2 | 0 | -9.5850755 | 0.005 | 0.389 | 0 |
| Fgl2 | 0 | -4.6728295 | 0.025 | 0.442 | 0 |
| Irgm1 | 0 | -3.3847754 | 0.084 | 0.549 | 0 |
| Slc38a6 | 0 | -0.7939891 | 0.369 | 0.894 | 0 |
| Ctsz | 0 | -1.3676100 | 0.552 | 0.947 | 0 |
| Nlrc5 | 0 | -5.0470359 | 0.020 | 0.425 | 0 |
| Ppp2r5a | 0 | -1.2606889 | 0.182 | 0.743 | 0 |
| AU020206 | 0 | -2.2173204 | 0.172 | 0.690 | 0 |
| Samhd1 | 0 | -1.1072513 | 0.177 | 0.717 | 0 |
| Psap | 0 | -1.2073459 | 0.626 | 0.973 | 0 |
| Serpine2 | 0 | -1.6291886 | 0.369 | 0.876 | 0 |
| Ctsh | 0 | -0.1872340 | 0.379 | 0.885 | 0 |
| Serf2 | 0 | -0.9470411 | 0.182 | 0.752 | 0 |
| Grn | 0 | -1.2197911 | 0.473 | 0.938 | 0 |
| Irf7 | 0 | -7.5365346 | 0.015 | 0.398 | 0 |
| Scamp2 | 0 | -0.8571562 | 0.296 | 0.796 | 0 |
| Rsrp1 | 0 | -1.0764042 | 0.468 | 0.956 | 0 |
| Parp14 | 0 | -5.8054336 | 0.099 | 0.531 | 0 |
| Slfn8 | 0 | -1.3030567 | 0.167 | 0.673 | 0 |
| Ctsb | 0 | -1.1516067 | 0.586 | 0.965 | 0 |
| Tmcc3 | 0 | -1.4966226 | 0.118 | 0.628 | 0 |
| Oas1g | 0 | -4.0795742 | 0.020 | 0.407 | 0 |
| Hexa | 0 | -0.9593763 | 0.409 | 0.894 | 0 |
| Hsp90b1 | 0 | -0.4787846 | 0.330 | 0.858 | 0 |
| C1qa | 0 | -1.2082081 | 0.675 | 1.000 | 0 |
| Zfp488 | 0 | -1.5944163 | 0.192 | 0.752 | 0 |
| C1qc | 0 | -1.1968656 | 0.729 | 0.991 | 0 |
| Hmmr | 0 | -1.7717395 | 0.094 | 0.558 | 0 |
| Ncl | 0 | -1.4222573 | 0.236 | 0.752 | 0 |
| Psme1 | 0 | -2.0139909 | 0.099 | 0.540 | 0 |
| Laptm5 | 0 | -1.2177837 | 0.665 | 0.965 | 0 |
| Ifi207 | 0 | -8.7601559 | 0.005 | 0.354 | 0 |
| Cd9 | 0 | -1.4140766 | 0.537 | 0.938 | 0 |
| Ifi208 | 0 | -4.3919174 | 0.054 | 0.469 | 0 |
| Isg15 | 0 | -4.2016957 | 0.054 | 0.460 | 0 |
| Sgk3 | 0 | -1.5027511 | 0.138 | 0.646 | 0 |
| Man2b1 | 0 | -0.9043467 | 0.399 | 0.885 | 0 |
| Dcbld2 | 0 | 0.1416245 | 0.227 | 0.761 | 0 |
| Rpl18a | 0 | -0.6125305 | 0.389 | 0.947 | 0 |
| Sema4d | 0 | -1.7259783 | 0.187 | 0.681 | 0 |
| Csf3r | 0 | -1.7711726 | 0.330 | 0.814 | 0 |
| Parp9 | 0 | -4.0149973 | 0.020 | 0.389 | 0 |
| Pikfyve | 0 | -0.5615008 | 0.296 | 0.858 | 0 |
| Tmbim6 | 0 | -1.4821522 | 0.365 | 0.841 | 0 |
| Ncf2 | 0 | -0.1795121 | 0.222 | 0.735 | 0 |
| Pdia3 | 0 | -1.0344954 | 0.325 | 0.823 | 0 |
| Herc6 | 0 | -1.4670957 | 0.207 | 0.681 | 0 |
| Atf2 | 0 | -1.2207374 | 0.113 | 0.558 | 0 |
| Ifi214 | 0 | -3.9696484 | 0.049 | 0.451 | 0 |
| Stat2 | 0 | -2.8637168 | 0.158 | 0.619 | 0 |
| Slfn9 | 0 | -2.6545765 | 0.167 | 0.681 | 0 |
| Eif2ak2 | 0 | -0.8729874 | 0.286 | 0.779 | 0 |
| Unc93b1 | 0 | -0.6736716 | 0.365 | 0.894 | 0 |
| Lag3 | 0 | -1.3185418 | 0.340 | 0.814 | 0 |
| Tmem234 | 0 | -2.0836862 | 0.212 | 0.717 | 0 |
| Zbp1 | 0 | -6.5769951 | 0.015 | 0.363 | 0 |
| Acot4 | 0 | 0.4015670 | 0.158 | 0.611 | 0 |
| Fcgr2b | 0 | -0.5420644 | 0.300 | 0.867 | 0 |
| Sfi1 | 0 | -1.9027834 | 0.291 | 0.779 | 0 |
Microglia3_vs_Microglia5
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-70.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Cd74 | 0 | -9.3853200 | 0.039 | 0.959 | 0 |
| H2-Ab1 | 0 | -11.8268781 | 0.015 | 0.904 | 0 |
| H2-Aa | 0 | -9.3473696 | 0.039 | 0.712 | 0 |
| H2-Eb1 | 0 | -10.4594799 | 0.010 | 0.630 | 0 |
| H2-D1 | 0 | -3.4064078 | 0.355 | 0.959 | 0 |
| H2-K1 | 0 | -2.4994716 | 0.389 | 0.932 | 0 |
| Serpine2 | 0 | -2.1643977 | 0.369 | 0.904 | 0 |
| H2-T23 | 0 | -2.7260109 | 0.281 | 0.808 | 0 |
| Ctsd | 0 | -1.8135953 | 0.793 | 0.973 | 0 |
| Laptm5 | 0 | -1.5295736 | 0.665 | 0.986 | 0 |
| Mef2c | 0 | -1.2526086 | 0.310 | 0.904 | 0 |
| Rab3gap1 | 0 | -1.4954167 | 0.207 | 0.781 | 0 |
| Eif2a | 0 | 4.5455464 | 0.941 | 0.808 | 0 |
| Psap | 0 | -1.3221645 | 0.626 | 0.986 | 0 |
| Rps2 | 0 | -2.2932708 | 0.128 | 0.630 | 0 |
| C1qa | 0 | -1.3886649 | 0.675 | 1.000 | 0 |
| Syngr1 | 0 | -2.3381513 | 0.256 | 0.753 | 0 |
| Vmn1r13 | 0 | 5.3286250 | 0.946 | 0.726 | 0 |
| Csf3r | 0 | -2.0938980 | 0.330 | 0.849 | 0 |
| Ly86 | 0 | -1.0619285 | 0.512 | 0.986 | 0 |
| AU020206 | 0 | -2.5151180 | 0.172 | 0.671 | 0 |
| Ctsb | 0 | -1.5250075 | 0.586 | 0.959 | 0 |
| Tmbim6 | 0 | -1.6714603 | 0.365 | 0.877 | 0 |
| Cd9 | 0 | -1.5060192 | 0.537 | 0.945 | 0 |
| C1qc | 0 | -1.3153308 | 0.729 | 1.000 | 0 |
| Man2b1 | 0 | -1.1501960 | 0.399 | 0.890 | 0 |
| Trem2 | 0 | -1.3833079 | 0.527 | 0.973 | 0 |
| Or8b44 | 0 | 7.1029906 | 0.921 | 0.726 | 0 |
| Ly6e | 0 | -1.9107258 | 0.404 | 0.863 | 0 |
| Dnajb14 | 0 | -1.7303235 | 0.177 | 0.685 | 0 |
| Fth1 | 0 | -0.9345402 | 0.581 | 1.000 | 0 |
| Tyrobp | 0 | -1.7597110 | 0.562 | 0.973 | 0 |
| Lrp1 | 0 | -1.5176647 | 0.271 | 0.795 | 0 |
| Hnrnpc | 0 | -2.3097710 | 0.172 | 0.685 | 0 |
| H2-Oa | 0 | -4.9356767 | 0.020 | 0.356 | 0 |
| Mpeg1 | 0 | -1.1099886 | 0.404 | 0.918 | 0 |
| Ppp2r5a | 0 | -1.7063703 | 0.182 | 0.685 | 0 |
| Arhgef40 | 0 | -0.6717269 | 0.251 | 0.781 | 0 |
| Inpp5d | 0 | -0.6580027 | 0.355 | 0.877 | 0 |
| Hexa | 0 | -1.2092582 | 0.409 | 0.877 | 0 |
| Tbxas1 | 0 | -1.1538932 | 0.192 | 0.699 | 0 |
| Ctsa | 0 | -0.8830622 | 0.502 | 0.945 | 0 |
| Man2b2 | 0 | -3.6810408 | 0.034 | 0.384 | 0 |
| Stx7 | 0 | -0.7127254 | 0.212 | 0.712 | 0 |
| Ctsh | 0 | -0.2188387 | 0.379 | 0.836 | 0 |
| St14 | 0 | 0.3535673 | 0.177 | 0.685 | 0 |
| Pafah1b1 | 0 | -1.6140958 | 0.064 | 0.452 | 0 |
| Elob | 0 | -0.7162583 | 0.113 | 0.562 | 0 |
| Gsk3b | 0 | -0.7844757 | 0.207 | 0.726 | 0 |
| Uspl1 | 0 | -2.3443760 | 0.044 | 0.411 | 0 |
| Sh3bgrl3 | 0 | -0.8573382 | 0.167 | 0.658 | 0 |
| Psmb8 | 0 | -1.2594989 | 0.108 | 0.562 | 0 |
| Rnase4 | 0 | -1.0772526 | 0.488 | 0.932 | 0 |
| Ccni | 0 | -0.3496484 | 0.099 | 0.548 | 0 |
| Rabgap1l | 0 | -2.0658830 | 0.163 | 0.630 | 0 |
| Alg5 | 0 | -1.9154445 | 0.089 | 0.507 | 0 |
| Lipe | 0 | 4.1779459 | 0.975 | 0.836 | 0 |
| H2-Q7 | 0 | -2.7364203 | 0.172 | 0.603 | 0 |
| Grn | 0 | -1.1976512 | 0.473 | 0.890 | 0 |
| Tmed10 | 0 | -1.2438598 | 0.192 | 0.671 | 0 |
| Cdk9 | 0 | -1.0995925 | 0.064 | 0.438 | 0 |
| Trac | 0 | 5.3777173 | 0.823 | 0.644 | 0 |
| Bin1 | 0 | -0.4103864 | 0.227 | 0.740 | 0 |
| Ctss | 0 | -0.9825570 | 0.847 | 1.000 | 0 |
| Cd68 | 0 | -0.5978695 | 0.399 | 0.877 | 0 |
| Glmp | 0 | -1.4176084 | 0.197 | 0.658 | 0 |
| Unc93b1 | 0 | -0.8150072 | 0.365 | 0.863 | 0 |
| Ubl5 | 0 | -0.0670143 | 0.153 | 0.603 | 0 |
| Ftl1 | 0 | -0.9576266 | 0.517 | 0.973 | 0 |
| Gng5 | 0 | -1.2399232 | 0.099 | 0.534 | 0 |
| C1qb | 0 | -1.1289828 | 0.749 | 0.986 | 0 |
| Csf1r | 0 | -1.0827861 | 0.759 | 1.000 | 0 |
| Fyb1 | 0 | -1.1133807 | 0.241 | 0.740 | 0 |
| H2-Q10 | 0 | -1.7575812 | 0.172 | 0.630 | 0 |
| Dnajc12 | 0 | -1.8431548 | 0.108 | 0.534 | 0 |
| Atp6v0c | 0 | -1.5373524 | 0.296 | 0.740 | 0 |
| Rnaset2a | 0 | -1.0878674 | 0.325 | 0.836 | 0 |
| Rps16-ps2 | 0 | -1.4871292 | 0.128 | 0.575 | 0 |
| Cd300c2 | 0 | -0.5001927 | 0.217 | 0.699 | 0 |
| H2-DMa | 0 | -1.4773021 | 0.167 | 0.589 | 0 |
| H2-M3 | 0 | -1.9527795 | 0.054 | 0.411 | 0 |
| Efhd2 | 0 | -1.1526676 | 0.158 | 0.575 | 0 |
| Slc46a3 | 0 | -2.1091092 | 0.059 | 0.411 | 0 |
| Arfgef3 | 0 | 3.9909418 | 0.833 | 0.658 | 0 |
| Fcgr1 | 0 | -1.1192498 | 0.232 | 0.685 | 0 |
| mt-Nd4l | 0 | -0.9938295 | 0.222 | 0.685 | 0 |
| Axl | 0 | -7.7884321 | 0.020 | 0.301 | 0 |
| Rac1 | 0 | -0.7403408 | 0.266 | 0.767 | 0 |
| Cux2 | 0 | 4.1262726 | 0.906 | 0.795 | 0 |
| Cep290 | 0 | 3.9076848 | 0.926 | 0.712 | 0 |
| Sdf4 | 0 | -2.0023669 | 0.143 | 0.548 | 0 |
| Ypel3 | 0 | -1.9443241 | 0.108 | 0.507 | 0 |
| Rhoa | 0 | -0.6505675 | 0.315 | 0.808 | 0 |
| Mlph | 0 | -2.7315945 | 0.133 | 0.575 | 0 |
| Usp12 | 0 | -3.7514392 | 0.074 | 0.425 | 0 |
| Ywhah | 0 | -0.5799454 | 0.389 | 0.863 | 0 |
| H2-Q6 | 0 | -2.5397005 | 0.103 | 0.493 | 0 |
| Ctsz | 0 | -1.3705490 | 0.552 | 0.890 | 0 |
| Pld1 | 0 | -1.9528670 | 0.256 | 0.712 | 0 |
| Fcgr2b | 0 | -0.9513862 | 0.300 | 0.781 | 0 |
Microglia3_vs_Microglia5_comorbid
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-73.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| Cd74 | 0 | -9.3853200 | 0.039 | 0.959 | 0 |
| H2-Ab1 | 0 | -11.8268781 | 0.015 | 0.904 | 0 |
| H2-Aa | 0 | -9.3473696 | 0.039 | 0.712 | 0 |
| H2-Eb1 | 0 | -10.4594799 | 0.010 | 0.630 | 0 |
| H2-D1 | 0 | -3.4064078 | 0.355 | 0.959 | 0 |
| H2-K1 | 0 | -2.4994716 | 0.389 | 0.932 | 0 |
| Serpine2 | 0 | -2.1643977 | 0.369 | 0.904 | 0 |
| H2-T23 | 0 | -2.7260109 | 0.281 | 0.808 | 0 |
| Ctsd | 0 | -1.8135953 | 0.793 | 0.973 | 0 |
| Laptm5 | 0 | -1.5295736 | 0.665 | 0.986 | 0 |
| Mef2c | 0 | -1.2526086 | 0.310 | 0.904 | 0 |
| Rab3gap1 | 0 | -1.4954167 | 0.207 | 0.781 | 0 |
| Eif2a | 0 | 4.5455464 | 0.941 | 0.808 | 0 |
| Psap | 0 | -1.3221645 | 0.626 | 0.986 | 0 |
| Rps2 | 0 | -2.2932708 | 0.128 | 0.630 | 0 |
| C1qa | 0 | -1.3886649 | 0.675 | 1.000 | 0 |
| Syngr1 | 0 | -2.3381513 | 0.256 | 0.753 | 0 |
| Vmn1r13 | 0 | 5.3286250 | 0.946 | 0.726 | 0 |
| Csf3r | 0 | -2.0938980 | 0.330 | 0.849 | 0 |
| Ly86 | 0 | -1.0619285 | 0.512 | 0.986 | 0 |
| AU020206 | 0 | -2.5151180 | 0.172 | 0.671 | 0 |
| Ctsb | 0 | -1.5250075 | 0.586 | 0.959 | 0 |
| Tmbim6 | 0 | -1.6714603 | 0.365 | 0.877 | 0 |
| Cd9 | 0 | -1.5060192 | 0.537 | 0.945 | 0 |
| C1qc | 0 | -1.3153308 | 0.729 | 1.000 | 0 |
| Man2b1 | 0 | -1.1501960 | 0.399 | 0.890 | 0 |
| Trem2 | 0 | -1.3833079 | 0.527 | 0.973 | 0 |
| Or8b44 | 0 | 7.1029906 | 0.921 | 0.726 | 0 |
| Ly6e | 0 | -1.9107258 | 0.404 | 0.863 | 0 |
| Dnajb14 | 0 | -1.7303235 | 0.177 | 0.685 | 0 |
| Fth1 | 0 | -0.9345402 | 0.581 | 1.000 | 0 |
| Tyrobp | 0 | -1.7597110 | 0.562 | 0.973 | 0 |
| Lrp1 | 0 | -1.5176647 | 0.271 | 0.795 | 0 |
| Hnrnpc | 0 | -2.3097710 | 0.172 | 0.685 | 0 |
| H2-Oa | 0 | -4.9356767 | 0.020 | 0.356 | 0 |
| Mpeg1 | 0 | -1.1099886 | 0.404 | 0.918 | 0 |
| Ppp2r5a | 0 | -1.7063703 | 0.182 | 0.685 | 0 |
| Arhgef40 | 0 | -0.6717269 | 0.251 | 0.781 | 0 |
| Inpp5d | 0 | -0.6580027 | 0.355 | 0.877 | 0 |
| Hexa | 0 | -1.2092582 | 0.409 | 0.877 | 0 |
| Tbxas1 | 0 | -1.1538932 | 0.192 | 0.699 | 0 |
| Ctsa | 0 | -0.8830622 | 0.502 | 0.945 | 0 |
| Man2b2 | 0 | -3.6810408 | 0.034 | 0.384 | 0 |
| Stx7 | 0 | -0.7127254 | 0.212 | 0.712 | 0 |
| Ctsh | 0 | -0.2188387 | 0.379 | 0.836 | 0 |
| St14 | 0 | 0.3535673 | 0.177 | 0.685 | 0 |
| Pafah1b1 | 0 | -1.6140958 | 0.064 | 0.452 | 0 |
| Elob | 0 | -0.7162583 | 0.113 | 0.562 | 0 |
| Gsk3b | 0 | -0.7844757 | 0.207 | 0.726 | 0 |
| Uspl1 | 0 | -2.3443760 | 0.044 | 0.411 | 0 |
| Sh3bgrl3 | 0 | -0.8573382 | 0.167 | 0.658 | 0 |
| Psmb8 | 0 | -1.2594989 | 0.108 | 0.562 | 0 |
| Rnase4 | 0 | -1.0772526 | 0.488 | 0.932 | 0 |
| Ccni | 0 | -0.3496484 | 0.099 | 0.548 | 0 |
| Rabgap1l | 0 | -2.0658830 | 0.163 | 0.630 | 0 |
| Alg5 | 0 | -1.9154445 | 0.089 | 0.507 | 0 |
| Lipe | 0 | 4.1779459 | 0.975 | 0.836 | 0 |
| H2-Q7 | 0 | -2.7364203 | 0.172 | 0.603 | 0 |
| Grn | 0 | -1.1976512 | 0.473 | 0.890 | 0 |
| Tmed10 | 0 | -1.2438598 | 0.192 | 0.671 | 0 |
| Cdk9 | 0 | -1.0995925 | 0.064 | 0.438 | 0 |
| Trac | 0 | 5.3777173 | 0.823 | 0.644 | 0 |
| Bin1 | 0 | -0.4103864 | 0.227 | 0.740 | 0 |
| Ctss | 0 | -0.9825570 | 0.847 | 1.000 | 0 |
| Cd68 | 0 | -0.5978695 | 0.399 | 0.877 | 0 |
| Glmp | 0 | -1.4176084 | 0.197 | 0.658 | 0 |
| Unc93b1 | 0 | -0.8150072 | 0.365 | 0.863 | 0 |
| Ubl5 | 0 | -0.0670143 | 0.153 | 0.603 | 0 |
| Ftl1 | 0 | -0.9576266 | 0.517 | 0.973 | 0 |
| Gng5 | 0 | -1.2399232 | 0.099 | 0.534 | 0 |
| C1qb | 0 | -1.1289828 | 0.749 | 0.986 | 0 |
| Csf1r | 0 | -1.0827861 | 0.759 | 1.000 | 0 |
| Fyb1 | 0 | -1.1133807 | 0.241 | 0.740 | 0 |
| H2-Q10 | 0 | -1.7575812 | 0.172 | 0.630 | 0 |
| Dnajc12 | 0 | -1.8431548 | 0.108 | 0.534 | 0 |
| Atp6v0c | 0 | -1.5373524 | 0.296 | 0.740 | 0 |
| Rnaset2a | 0 | -1.0878674 | 0.325 | 0.836 | 0 |
| Rps16-ps2 | 0 | -1.4871292 | 0.128 | 0.575 | 0 |
| Cd300c2 | 0 | -0.5001927 | 0.217 | 0.699 | 0 |
| H2-DMa | 0 | -1.4773021 | 0.167 | 0.589 | 0 |
| H2-M3 | 0 | -1.9527795 | 0.054 | 0.411 | 0 |
| Efhd2 | 0 | -1.1526676 | 0.158 | 0.575 | 0 |
| Slc46a3 | 0 | -2.1091092 | 0.059 | 0.411 | 0 |
| Arfgef3 | 0 | 3.9909418 | 0.833 | 0.658 | 0 |
| Fcgr1 | 0 | -1.1192498 | 0.232 | 0.685 | 0 |
| mt-Nd4l | 0 | -0.9938295 | 0.222 | 0.685 | 0 |
| Axl | 0 | -7.7884321 | 0.020 | 0.301 | 0 |
| Rac1 | 0 | -0.7403408 | 0.266 | 0.767 | 0 |
| Cux2 | 0 | 4.1262726 | 0.906 | 0.795 | 0 |
| Cep290 | 0 | 3.9076848 | 0.926 | 0.712 | 0 |
| Sdf4 | 0 | -2.0023669 | 0.143 | 0.548 | 0 |
| Ypel3 | 0 | -1.9443241 | 0.108 | 0.507 | 0 |
| Rhoa | 0 | -0.6505675 | 0.315 | 0.808 | 0 |
| Mlph | 0 | -2.7315945 | 0.133 | 0.575 | 0 |
| Usp12 | 0 | -3.7514392 | 0.074 | 0.425 | 0 |
| Ywhah | 0 | -0.5799454 | 0.389 | 0.863 | 0 |
| H2-Q6 | 0 | -2.5397005 | 0.103 | 0.493 | 0 |
| Ctsz | 0 | -1.3705490 | 0.552 | 0.890 | 0 |
| Pld1 | 0 | -1.9528670 | 0.256 | 0.712 | 0 |
| Fcgr2b | 0 | -0.9513862 | 0.300 | 0.781 | 0 |
Microglia4_vs_Microglia5
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-76.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| H2-Ab1 | 0.0000000 | -6.7180526 | 0.035 | 0.904 | 0.0000000 |
| Cd74 | 0.0000000 | -4.8209626 | 0.257 | 0.959 | 0.0000000 |
| H2-Aa | 0.0000000 | -6.0375032 | 0.106 | 0.712 | 0.0000000 |
| H2-Eb1 | 0.0000000 | -6.1621051 | 0.027 | 0.630 | 0.0000000 |
| Ifit3 | 0.0000000 | 7.0195252 | 0.628 | 0.068 | 0.0000000 |
| Rtp4 | 0.0000000 | 2.8367076 | 0.717 | 0.110 | 0.0000000 |
| Ccl12 | 0.0000000 | 4.2299540 | 0.690 | 0.219 | 0.0000002 |
| Trim30a | 0.0000000 | 2.7661848 | 0.726 | 0.315 | 0.0000012 |
| Oasl2 | 0.0000000 | 3.5298771 | 0.673 | 0.247 | 0.0000017 |
| Mx1 | 0.0000000 | 6.1274782 | 0.522 | 0.123 | 0.0000217 |
| Iigp1 | 0.0000000 | 5.0499900 | 0.558 | 0.123 | 0.0000218 |
| Ifit3b | 0.0000000 | 6.7744205 | 0.504 | 0.110 | 0.0000589 |
| Stat1 | 0.0000000 | 1.8550486 | 0.823 | 0.466 | 0.0001113 |
| Ifi204 | 0.0000000 | 2.3550192 | 0.726 | 0.342 | 0.0001307 |
| Iigp1c | 0.0000000 | 3.8414881 | 0.602 | 0.247 | 0.0001452 |
| Ifitm3 | 0.0000000 | 2.9768778 | 0.566 | 0.178 | 0.0002150 |
| Ifi213 | 0.0000000 | 3.5047205 | 0.513 | 0.137 | 0.0004443 |
| Herc6 | 0.0000001 | 3.0351022 | 0.681 | 0.329 | 0.0012795 |
| Ifi207 | 0.0000002 | 6.5949625 | 0.354 | 0.027 | 0.0028926 |
| H2-D1 | 0.0000002 | -0.9420868 | 0.903 | 0.959 | 0.0034501 |
| Ifit2 | 0.0000003 | 4.0745665 | 0.425 | 0.082 | 0.0042823 |
| Ifit1 | 0.0000003 | 6.7083986 | 0.363 | 0.041 | 0.0042910 |
| Rnf213 | 0.0000003 | 1.8843658 | 0.628 | 0.219 | 0.0055075 |
| Slfn5 | 0.0000003 | 3.7764428 | 0.717 | 0.411 | 0.0055480 |
| Ifi206 | 0.0000005 | 5.8695650 | 0.319 | 0.014 | 0.0076853 |
| Irf7 | 0.0000006 | 3.4349045 | 0.398 | 0.068 | 0.0091566 |
| Oas1a | 0.0000006 | 2.7870148 | 0.460 | 0.110 | 0.0092512 |
| Usp18 | 0.0000007 | 3.5866099 | 0.504 | 0.178 | 0.0104704 |
| Ifi214 | 0.0000014 | 3.4416636 | 0.451 | 0.123 | 0.0216193 |
| Ifi209 | 0.0000021 | 3.3992342 | 0.469 | 0.164 | 0.0339346 |
| Xaf1 | 0.0000029 | 2.5088532 | 0.708 | 0.479 | 0.0461421 |
| Trex1 | 0.0000033 | 1.7773015 | 0.575 | 0.247 | 0.0529762 |
| Oas2 | 0.0000046 | 3.7831455 | 0.327 | 0.041 | 0.0727644 |
| Ifi208 | 0.0000048 | 3.2651998 | 0.469 | 0.137 | 0.0758662 |
| Phf11a | 0.0000063 | 3.4932374 | 0.345 | 0.055 | 0.1003983 |
| Tgtp2 | 0.0000064 | 2.8919153 | 0.389 | 0.096 | 0.1013408 |
| Ifi211 | 0.0000092 | 5.1271647 | 0.283 | 0.027 | 0.1474082 |
| Atp6v0a2 | 0.0000141 | 0.8873805 | 0.575 | 0.219 | 0.2245107 |
| Phf11b | 0.0000186 | 2.1541175 | 0.389 | 0.110 | 0.2966558 |
| Trim30d | 0.0000190 | 1.7855877 | 0.584 | 0.301 | 0.3036422 |
| Sp100 | 0.0000281 | 2.9139929 | 0.611 | 0.384 | 0.4482600 |
| Nlrc5 | 0.0000296 | 2.4676577 | 0.425 | 0.137 | 0.4716227 |
| Slfn8 | 0.0000348 | 2.1642037 | 0.673 | 0.438 | 0.5542296 |
| Hmmr | 0.0000359 | 1.8791510 | 0.558 | 0.260 | 0.5717086 |
| Mx2 | 0.0000393 | 2.4805586 | 0.310 | 0.055 | 0.6265144 |
| Rigi | 0.0000457 | 3.7083975 | 0.673 | 0.521 | 0.7294898 |
| Gvin2 | 0.0000544 | 1.9577801 | 0.593 | 0.288 | 0.8675028 |
| Oas1g | 0.0000562 | 0.8679367 | 0.407 | 0.123 | 0.8958727 |
| Rsad2 | 0.0000608 | 5.9794145 | 0.319 | 0.082 | 0.9692005 |
| Zc3hav1 | 0.0000620 | 2.3535287 | 0.549 | 0.315 | 0.9885789 |
| Helz2 | 0.0000658 | 6.4845820 | 0.195 | 0.000 | 1.0000000 |
| Isg20 | 0.0000658 | 5.4635086 | 0.195 | 0.000 | 1.0000000 |
| Znfx1 | 0.0000670 | 1.9058425 | 0.522 | 0.233 | 1.0000000 |
| Slfn2 | 0.0000677 | 3.4773890 | 0.487 | 0.260 | 1.0000000 |
| Ms4a6b | 0.0000708 | 2.5057945 | 0.460 | 0.205 | 1.0000000 |
| Ifi27l2a | 0.0000719 | 1.7247806 | 0.540 | 0.288 | 1.0000000 |
| Zbp1 | 0.0000729 | 2.6578431 | 0.363 | 0.110 | 1.0000000 |
| Irgm1 | 0.0000840 | 1.8493220 | 0.549 | 0.301 | 1.0000000 |
| Uba7 | 0.0000842 | 1.6283294 | 0.487 | 0.205 | 1.0000000 |
| Isg15 | 0.0001044 | 2.5363107 | 0.460 | 0.219 | 1.0000000 |
| Bst2 | 0.0001222 | 1.2376012 | 0.558 | 0.274 | 1.0000000 |
| Gvin1 | 0.0001611 | 1.8656888 | 0.593 | 0.288 | 1.0000000 |
| Pml | 0.0001896 | 4.3797669 | 0.336 | 0.110 | 1.0000000 |
| Trafd1 | 0.0002011 | 1.5602221 | 0.496 | 0.233 | 1.0000000 |
| Nmi | 0.0002139 | 2.1638684 | 0.292 | 0.068 | 1.0000000 |
| Tor3a | 0.0002248 | 1.7232841 | 0.496 | 0.247 | 1.0000000 |
| Lgals3bp | 0.0002429 | 0.8641333 | 0.814 | 0.548 | 1.0000000 |
| Gbp9 | 0.0002674 | 3.3944098 | 0.283 | 0.068 | 1.0000000 |
| Phf11d | 0.0002699 | 1.8343718 | 0.442 | 0.192 | 1.0000000 |
| Parp9 | 0.0002977 | 3.1895987 | 0.389 | 0.164 | 1.0000000 |
| BC005537 | 0.0003186 | 1.5327808 | 0.566 | 0.329 | 1.0000000 |
| Parp14 | 0.0003618 | 1.7364523 | 0.531 | 0.288 | 1.0000000 |
| Etnk1 | 0.0003639 | 1.0706114 | 0.575 | 0.315 | 1.0000000 |
| Cacna2d3 | 0.0003645 | 2.8377693 | 0.212 | 0.027 | 1.0000000 |
| Bglap3 | 0.0004380 | 1.7114147 | 0.186 | 0.014 | 1.0000000 |
| Gvin-ps7 | 0.0004522 | 2.0859611 | 0.558 | 0.342 | 1.0000000 |
| Slc25a23 | 0.0004737 | 1.6030931 | 0.301 | 0.082 | 1.0000000 |
| Eif2ak2 | 0.0004816 | 1.3339524 | 0.779 | 0.616 | 1.0000000 |
| Pim1 | 0.0005341 | 1.0745068 | 0.310 | 0.096 | 1.0000000 |
| Fcgr1 | 0.0005507 | 0.5304902 | 0.850 | 0.685 | 1.0000000 |
| Syngr1 | 0.0005960 | -0.8745693 | 0.611 | 0.753 | 1.0000000 |
| Oasl1 | 0.0006350 | 3.6416291 | 0.177 | 0.014 | 1.0000000 |
| Yeats2 | 0.0006850 | 1.0615890 | 0.434 | 0.164 | 1.0000000 |
| Usp12 | 0.0007114 | -1.7635080 | 0.212 | 0.425 | 1.0000000 |
| Or4m1 | 0.0007203 | 0.8873351 | 0.558 | 0.288 | 1.0000000 |
| Ddx60 | 0.0007856 | 3.2313260 | 0.381 | 0.178 | 1.0000000 |
| Rpl27rt | 0.0007948 | 1.1872376 | 0.407 | 0.164 | 1.0000000 |
| Dhx58 | 0.0008764 | 2.2083221 | 0.398 | 0.192 | 1.0000000 |
| Tbc1d17 | 0.0008837 | -1.9752687 | 0.212 | 0.438 | 1.0000000 |
| Rdh14 | 0.0009081 | 2.5239321 | 0.221 | 0.041 | 1.0000000 |
| Hspa4 | 0.0009162 | 1.5970181 | 0.319 | 0.110 | 1.0000000 |
| Sass6 | 0.0009514 | 3.0759238 | 0.779 | 0.616 | 1.0000000 |
| Mmp12 | 0.0009588 | 1.2198362 | 0.575 | 0.315 | 1.0000000 |
| Smg9 | 0.0009894 | 2.7966054 | 0.451 | 0.233 | 1.0000000 |
| Zfp12 | 0.0011424 | 4.3757188 | 0.274 | 0.082 | 1.0000000 |
| Cmtm8 | 0.0011483 | -3.4758316 | 0.088 | 0.260 | 1.0000000 |
| Mtmr12 | 0.0012256 | 0.0965453 | 0.124 | 0.329 | 1.0000000 |
| Ndufb2 | 0.0012750 | 2.6197800 | 0.513 | 0.315 | 1.0000000 |
| Cnga3 | 0.0012920 | 1.4220726 | 0.319 | 0.110 | 1.0000000 |
| Prkcd | 0.0013160 | 0.6385280 | 0.717 | 0.493 | 1.0000000 |
Microglia4_vs_Microglia5_comorbid
\(`1`
<img
src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-113-79.png"
width="960" style="display: block; margin: auto;"
/>\)2
attr(,“class”) [1] “list” “ggarrange”
Markers
| p_val | avg_log2FC | pct.1 | pct.2 | p_val_adj | |
|---|---|---|---|---|---|
| H2-Ab1 | 0.0000000 | -6.7180526 | 0.035 | 0.904 | 0.0000000 |
| Cd74 | 0.0000000 | -4.8209626 | 0.257 | 0.959 | 0.0000000 |
| H2-Aa | 0.0000000 | -6.0375032 | 0.106 | 0.712 | 0.0000000 |
| H2-Eb1 | 0.0000000 | -6.1621051 | 0.027 | 0.630 | 0.0000000 |
| Ifit3 | 0.0000000 | 7.0195252 | 0.628 | 0.068 | 0.0000000 |
| Rtp4 | 0.0000000 | 2.8367076 | 0.717 | 0.110 | 0.0000000 |
| Ccl12 | 0.0000000 | 4.2299540 | 0.690 | 0.219 | 0.0000002 |
| Trim30a | 0.0000000 | 2.7661848 | 0.726 | 0.315 | 0.0000012 |
| Oasl2 | 0.0000000 | 3.5298771 | 0.673 | 0.247 | 0.0000017 |
| Mx1 | 0.0000000 | 6.1274782 | 0.522 | 0.123 | 0.0000217 |
| Iigp1 | 0.0000000 | 5.0499900 | 0.558 | 0.123 | 0.0000218 |
| Ifit3b | 0.0000000 | 6.7744205 | 0.504 | 0.110 | 0.0000589 |
| Stat1 | 0.0000000 | 1.8550486 | 0.823 | 0.466 | 0.0001113 |
| Ifi204 | 0.0000000 | 2.3550192 | 0.726 | 0.342 | 0.0001307 |
| Iigp1c | 0.0000000 | 3.8414881 | 0.602 | 0.247 | 0.0001452 |
| Ifitm3 | 0.0000000 | 2.9768778 | 0.566 | 0.178 | 0.0002150 |
| Ifi213 | 0.0000000 | 3.5047205 | 0.513 | 0.137 | 0.0004443 |
| Herc6 | 0.0000001 | 3.0351022 | 0.681 | 0.329 | 0.0012795 |
| Ifi207 | 0.0000002 | 6.5949625 | 0.354 | 0.027 | 0.0028926 |
| H2-D1 | 0.0000002 | -0.9420868 | 0.903 | 0.959 | 0.0034501 |
| Ifit2 | 0.0000003 | 4.0745665 | 0.425 | 0.082 | 0.0042823 |
| Ifit1 | 0.0000003 | 6.7083986 | 0.363 | 0.041 | 0.0042910 |
| Rnf213 | 0.0000003 | 1.8843658 | 0.628 | 0.219 | 0.0055075 |
| Slfn5 | 0.0000003 | 3.7764428 | 0.717 | 0.411 | 0.0055480 |
| Ifi206 | 0.0000005 | 5.8695650 | 0.319 | 0.014 | 0.0076853 |
| Irf7 | 0.0000006 | 3.4349045 | 0.398 | 0.068 | 0.0091566 |
| Oas1a | 0.0000006 | 2.7870148 | 0.460 | 0.110 | 0.0092512 |
| Usp18 | 0.0000007 | 3.5866099 | 0.504 | 0.178 | 0.0104704 |
| Ifi214 | 0.0000014 | 3.4416636 | 0.451 | 0.123 | 0.0216193 |
| Ifi209 | 0.0000021 | 3.3992342 | 0.469 | 0.164 | 0.0339346 |
| Xaf1 | 0.0000029 | 2.5088532 | 0.708 | 0.479 | 0.0461421 |
| Trex1 | 0.0000033 | 1.7773015 | 0.575 | 0.247 | 0.0529762 |
| Oas2 | 0.0000046 | 3.7831455 | 0.327 | 0.041 | 0.0727644 |
| Ifi208 | 0.0000048 | 3.2651998 | 0.469 | 0.137 | 0.0758662 |
| Phf11a | 0.0000063 | 3.4932374 | 0.345 | 0.055 | 0.1003983 |
| Tgtp2 | 0.0000064 | 2.8919153 | 0.389 | 0.096 | 0.1013408 |
| Ifi211 | 0.0000092 | 5.1271647 | 0.283 | 0.027 | 0.1474082 |
| Atp6v0a2 | 0.0000141 | 0.8873805 | 0.575 | 0.219 | 0.2245107 |
| Phf11b | 0.0000186 | 2.1541175 | 0.389 | 0.110 | 0.2966558 |
| Trim30d | 0.0000190 | 1.7855877 | 0.584 | 0.301 | 0.3036422 |
| Sp100 | 0.0000281 | 2.9139929 | 0.611 | 0.384 | 0.4482600 |
| Nlrc5 | 0.0000296 | 2.4676577 | 0.425 | 0.137 | 0.4716227 |
| Slfn8 | 0.0000348 | 2.1642037 | 0.673 | 0.438 | 0.5542296 |
| Hmmr | 0.0000359 | 1.8791510 | 0.558 | 0.260 | 0.5717086 |
| Mx2 | 0.0000393 | 2.4805586 | 0.310 | 0.055 | 0.6265144 |
| Rigi | 0.0000457 | 3.7083975 | 0.673 | 0.521 | 0.7294898 |
| Gvin2 | 0.0000544 | 1.9577801 | 0.593 | 0.288 | 0.8675028 |
| Oas1g | 0.0000562 | 0.8679367 | 0.407 | 0.123 | 0.8958727 |
| Rsad2 | 0.0000608 | 5.9794145 | 0.319 | 0.082 | 0.9692005 |
| Zc3hav1 | 0.0000620 | 2.3535287 | 0.549 | 0.315 | 0.9885789 |
| Helz2 | 0.0000658 | 6.4845820 | 0.195 | 0.000 | 1.0000000 |
| Isg20 | 0.0000658 | 5.4635086 | 0.195 | 0.000 | 1.0000000 |
| Znfx1 | 0.0000670 | 1.9058425 | 0.522 | 0.233 | 1.0000000 |
| Slfn2 | 0.0000677 | 3.4773890 | 0.487 | 0.260 | 1.0000000 |
| Ms4a6b | 0.0000708 | 2.5057945 | 0.460 | 0.205 | 1.0000000 |
| Ifi27l2a | 0.0000719 | 1.7247806 | 0.540 | 0.288 | 1.0000000 |
| Zbp1 | 0.0000729 | 2.6578431 | 0.363 | 0.110 | 1.0000000 |
| Irgm1 | 0.0000840 | 1.8493220 | 0.549 | 0.301 | 1.0000000 |
| Uba7 | 0.0000842 | 1.6283294 | 0.487 | 0.205 | 1.0000000 |
| Isg15 | 0.0001044 | 2.5363107 | 0.460 | 0.219 | 1.0000000 |
| Bst2 | 0.0001222 | 1.2376012 | 0.558 | 0.274 | 1.0000000 |
| Gvin1 | 0.0001611 | 1.8656888 | 0.593 | 0.288 | 1.0000000 |
| Pml | 0.0001896 | 4.3797669 | 0.336 | 0.110 | 1.0000000 |
| Trafd1 | 0.0002011 | 1.5602221 | 0.496 | 0.233 | 1.0000000 |
| Nmi | 0.0002139 | 2.1638684 | 0.292 | 0.068 | 1.0000000 |
| Tor3a | 0.0002248 | 1.7232841 | 0.496 | 0.247 | 1.0000000 |
| Lgals3bp | 0.0002429 | 0.8641333 | 0.814 | 0.548 | 1.0000000 |
| Gbp9 | 0.0002674 | 3.3944098 | 0.283 | 0.068 | 1.0000000 |
| Phf11d | 0.0002699 | 1.8343718 | 0.442 | 0.192 | 1.0000000 |
| Parp9 | 0.0002977 | 3.1895987 | 0.389 | 0.164 | 1.0000000 |
| BC005537 | 0.0003186 | 1.5327808 | 0.566 | 0.329 | 1.0000000 |
| Parp14 | 0.0003618 | 1.7364523 | 0.531 | 0.288 | 1.0000000 |
| Etnk1 | 0.0003639 | 1.0706114 | 0.575 | 0.315 | 1.0000000 |
| Cacna2d3 | 0.0003645 | 2.8377693 | 0.212 | 0.027 | 1.0000000 |
| Bglap3 | 0.0004380 | 1.7114147 | 0.186 | 0.014 | 1.0000000 |
| Gvin-ps7 | 0.0004522 | 2.0859611 | 0.558 | 0.342 | 1.0000000 |
| Slc25a23 | 0.0004737 | 1.6030931 | 0.301 | 0.082 | 1.0000000 |
| Eif2ak2 | 0.0004816 | 1.3339524 | 0.779 | 0.616 | 1.0000000 |
| Pim1 | 0.0005341 | 1.0745068 | 0.310 | 0.096 | 1.0000000 |
| Fcgr1 | 0.0005507 | 0.5304902 | 0.850 | 0.685 | 1.0000000 |
| Syngr1 | 0.0005960 | -0.8745693 | 0.611 | 0.753 | 1.0000000 |
| Oasl1 | 0.0006350 | 3.6416291 | 0.177 | 0.014 | 1.0000000 |
| Yeats2 | 0.0006850 | 1.0615890 | 0.434 | 0.164 | 1.0000000 |
| Usp12 | 0.0007114 | -1.7635080 | 0.212 | 0.425 | 1.0000000 |
| Or4m1 | 0.0007203 | 0.8873351 | 0.558 | 0.288 | 1.0000000 |
| Ddx60 | 0.0007856 | 3.2313260 | 0.381 | 0.178 | 1.0000000 |
| Rpl27rt | 0.0007948 | 1.1872376 | 0.407 | 0.164 | 1.0000000 |
| Dhx58 | 0.0008764 | 2.2083221 | 0.398 | 0.192 | 1.0000000 |
| Tbc1d17 | 0.0008837 | -1.9752687 | 0.212 | 0.438 | 1.0000000 |
| Rdh14 | 0.0009081 | 2.5239321 | 0.221 | 0.041 | 1.0000000 |
| Hspa4 | 0.0009162 | 1.5970181 | 0.319 | 0.110 | 1.0000000 |
| Sass6 | 0.0009514 | 3.0759238 | 0.779 | 0.616 | 1.0000000 |
| Mmp12 | 0.0009588 | 1.2198362 | 0.575 | 0.315 | 1.0000000 |
| Smg9 | 0.0009894 | 2.7966054 | 0.451 | 0.233 | 1.0000000 |
| Zfp12 | 0.0011424 | 4.3757188 | 0.274 | 0.082 | 1.0000000 |
| Cmtm8 | 0.0011483 | -3.4758316 | 0.088 | 0.260 | 1.0000000 |
| Mtmr12 | 0.0012256 | 0.0965453 | 0.124 | 0.329 | 1.0000000 |
| Ndufb2 | 0.0012750 | 2.6197800 | 0.513 | 0.315 | 1.0000000 |
| Cnga3 | 0.0012920 | 1.4220726 | 0.319 | 0.110 | 1.0000000 |
| Prkcd | 0.0013160 | 0.6385280 | 0.717 | 0.493 | 1.0000000 |
within cluster Wt vs WT Stroke
[1] “Microglia0” [1] “Microglia2” [1] “Microglia3” [1] “no significant GO terms identified” [1] “Microglia5” [1] “Microglia4” [1] “no significant genes identified” [1] “Microglia1”
within cluster APPPS1_Stroke vs WT Stroke
[1] “Microglia0” [1] “no significant GO terms identified” [1] “Microglia2” [1] “Microglia3” [1] “no significant genes identified” [1] “Microglia5” [1] “no significant GO terms identified” [1] “Microglia4” [1] “no significant genes identified” [1] “Microglia1” [1] “no significant GO terms identified”
within cluster APPPS1 vs APPPS1 Stroke
[1] “Microglia0” [1] “Microglia2” [1] “no significant GO terms identified” [1] “Microglia3” [1] “no significant genes identified” [1] “Microglia5” [1] “Microglia4” [1] “no significant genes identified” [1] “Microglia1” [1] “no significant GO terms identified”
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 19005799 1015.1 30441271 1625.8 30441271 1625.8
Vcells 371263991 2832.6 728485830 5558.0 728485830 5558.0Pseudotime analysis
slinghsot starting Microglia 0
[1] "slingPseudotime_1"
[1] "slingPseudotime_2"
[1] "slingPseudotime_3"Look for genes that are up/down-regulated along pseudotime, for the re-clustered cells (Same paper Fig 2G/H)
Trajectory genes
By default, estimates of the spline coefficients are not returned as they are difficult to interpret. Rather, a log-fold change of expression along each path is estimated to provide some indication of the overall magnitude and direction of any change.
### WGCNA
In the paper https://www.nature.com/articles/s41586-018-0023-4 this analysis was used to generate different modules of gene lists that can then be mapped onto different treatment/genotypes within one experiment (see Figure 4). This is an analysis that can be done in Seurat https://smorabit.github.io/tutorials/9_scWGCNA_tutorial/ Which could be very cool for our data. In the paper they also have 3 different conditions in 2 genotypes.
avoid running this section as it takes very long
Allowing parallel execution with up to 7 working processes.pickSoftThreshold: will use block size 5277.
pickSoftThreshold: calculating connectivity for given powers...
..working on genes 1 through 5277 of 8478
..working on genes 5278 through 8478 of 8478
Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
1 1 0.884 -3.75 0.909 1.80e+02 1.63e+02 547.00
2 2 0.991 -2.51 0.996 8.15e+00 5.34e+00 93.20
3 3 0.976 -1.77 0.989 8.13e-01 2.36e-01 27.00
4 4 0.970 -1.47 0.990 1.75e-01 1.29e-02 12.80
5 5 0.940 -1.37 0.947 6.30e-02 8.42e-04 8.21
6 6 0.939 -1.30 0.938 3.02e-02 6.34e-05 6.00
7 7 0.970 -1.24 0.970 1.72e-02 5.37e-06 4.53
8 8 0.965 -1.20 0.956 1.10e-02 4.89e-07 3.50
9 9 0.427 -1.52 0.339 7.66e-03 4.85e-08 3.00
10 10 0.381 -1.73 0.273 5.70e-03 5.17e-09 3.00
11 12 0.433 -2.11 0.346 3.65e-03 6.21e-11 3.00
12 14 0.483 -2.22 0.358 2.70e-03 8.29e-13 3.00
13 16 0.518 -2.21 0.381 2.21e-03 1.15e-14 3.00
14 18 0.550 -2.16 0.483 1.93e-03 2.22e-16 3.00
15 20 0.568 -2.11 0.522 1.76e-03 0.00e+00 3.00
$nSets
[1] 1
$nGenes
[1] 8478
$nSamples
[1] 2944
$structureOK
[1] TRUE Calculating consensus modules and module eigengenes block-wise from all genes
Calculating topological overlaps block-wise from all genes
Flagging genes and samples with too many missing values...
..step 1
TOM calculation: adjacency..
..will use 7 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..Working on block 1 .
..Working on block 1 .
..merging consensus modules that are too close..
##### WGCNA by Genotype_treatment
WGCNA violin by condition
##### WGCNA violin by cluster
WGCNA Heatmap by condition
# A tibble: 20 × 10
# Groups: variable, Treatment [10]
variable Treatment Genotype avg_Eigenmodule sd_Eigenvalue med_Eigenvalue
<fct> <chr> <fct> <dbl> <dbl> <dbl>
1 MEyellow Ctrl WT -0.00766 0.0186 -0.00179
2 MEyellow Ctrl APPPS1 0.00710 0.0146 0.0101
3 MEyellow Stroke WT -0.00135 0.0187 0.00462
4 MEyellow Stroke APPPS1 0.00213 0.0184 0.00712
5 MEblue Ctrl WT 0.00759 0.0289 -0.00157
6 MEblue Ctrl APPPS1 -0.00337 0.00721 -0.00422
7 MEblue Stroke WT -0.00330 0.00616 -0.00396
8 MEblue Stroke APPPS1 -0.00209 0.0165 -0.00447
9 MEbrown Ctrl WT 0.00370 0.0239 0.000574
10 MEbrown Ctrl APPPS1 -0.00555 0.0139 -0.00445
11 MEbrown Stroke WT 0.00261 0.0170 0.00262
12 MEbrown Stroke APPPS1 -0.000289 0.0147 -0.00115
13 MEturquoise Ctrl WT 0.00368 0.0235 -0.00402
14 MEturquoise Ctrl APPPS1 -0.00121 0.0159 -0.00438
15 MEturquoise Stroke WT -0.00206 0.0126 -0.00364
16 MEturquoise Stroke APPPS1 -0.00109 0.0185 -0.00596
17 MEgrey Ctrl WT -0.00266 0.0220 -0.000564
18 MEgrey Ctrl APPPS1 0.00657 0.0153 0.00957
19 MEgrey Stroke WT -0.00456 0.0169 -0.000205
20 MEgrey Stroke APPPS1 -0.000372 0.0161 0.00324
# ℹ 4 more variables: pval <dbl>, pval_ast <chr>, Genotype_Treatment <fct>,
# Module <chr>png
2 
##### WGCNA Heatmap by cluster
# A tibble: 30 × 8
# Groups: variable [5]
variable labels avg_Eigenmodule sd_Eigenvalue med_Eigenvalue pval
<fct> <fct> <dbl> <dbl> <dbl> <dbl>
1 MEyellow Microglia0 0.00402 0.0114 0.00595 1.19e-274
2 MEyellow Microglia1 -0.00465 0.0179 0.000574 1.19e-274
3 MEyellow Microglia2 0.00968 0.0114 0.0123 1.19e-274
4 MEyellow Microglia3 -0.0359 0.0267 -0.0405 1.19e-274
5 MEyellow Microglia4 0.00616 0.0106 0.00890 1.19e-274
6 MEyellow Microglia5 0.00899 0.00909 0.00926 1.19e-274
7 MEblue Microglia0 -0.00124 0.00781 -0.00321 5.28e- 91
8 MEblue Microglia1 -0.00129 0.0137 -0.00412 5.28e- 91
9 MEblue Microglia2 -0.00408 0.00551 -0.00465 5.28e- 91
10 MEblue Microglia3 0.0247 0.0550 -0.00163 5.28e- 91
# ℹ 20 more rows
# ℹ 2 more variables: pval_ast <chr>, Module <chr>png
2 
Heatmaps Genewise per module
Heatmpas top 50 genes per module Conditions wise
[1] "blue" "brown" "grey" "turquoise" "yellow" png
2 png
2 png
2 png
2 Heatmpas top 50 genes per module Cluster wise
[1] "blue" "brown" "grey" "turquoise" "yellow" png
2 png
2 png
2 png
2 WGCNA GO terms
cell cylce scoring plots
Pairwise comparisons using t tests with pooled SD
data: metadata$S.Score and metadata$labels
Microglia0 Microglia1 Microglia2 Microglia3 Microglia4
Microglia1 1 - - - -
Microglia2 1 1 - - -
Microglia3 1 1 1 - -
Microglia4 1 1 1 1 -
Microglia5 1 1 1 1 1
P value adjustment method: holm
Pairwise comparisons using t tests with pooled SD
data: metadata$G2M.Score and metadata$labels
Microglia0 Microglia1 Microglia2 Microglia3 Microglia4
Microglia1 1.00 - - - -
Microglia2 0.95 0.50 - - -
Microglia3 1.00 1.00 1.00 - -
Microglia4 1.00 1.00 1.00 1.00 -
Microglia5 1.00 1.00 1.00 1.00 1.00
P value adjustment method: holm Rdigplot custom genes BAM CAM
BAM = “Cd36”, “CD38”,“Lyve1”,“Cd206”,“CD163”, “Cd169” CAM = “Emilin2”, “PF4”, “Ms4a”, “Hp”,“F5”,“Mki67”
#QC plots final set
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 18119463 967.7 30441271 1625.8 30441271 1625.8
Vcells 300451975 2292.3 875090551 6676.5 875090551 6676.5
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] TSCAN_1.44.0 ggbeeswarm_0.7.2
[3] chisq.posthoc.test_0.1.2 gprofiler2_0.2.3
[5] mclust_6.1.2 future_1.67.0
[7] ensembldb_2.30.0 AnnotationFilter_1.30.0
[9] GenomicFeatures_1.58.0 lm.beta_1.7-3
[11] pheatmap_1.0.13 RColorBrewer_1.1-3
[13] kableExtra_1.4.0 ggrepel_0.9.5
[15] knitr_1.50 org.Mm.eg.db_3.20.0
[17] AnnotationDbi_1.68.0 plotly_4.11.0
[19] WGCNA_1.74 fastcluster_1.3.0
[21] dynamicTreeCut_1.63-1 AnnotationHub_3.14.0
[23] BiocFileCache_2.14.0 dbplyr_2.5.1
[25] RCurl_1.98-1.17 clustree_0.5.1
[27] ggraph_2.2.2 ggpubr_0.6.1
[29] slingshot_2.14.0 TrajectoryUtils_1.14.0
[31] SingleCellExperiment_1.28.1 princurve_2.1.6
[33] DT_0.34.0 viridis_0.6.5
[35] viridisLite_0.4.2 openxlsx_4.2.8
[37] compareGroups_4.10.0 data.table_1.17.8
[39] SingleR_2.8.0 harmony_1.2.3
[41] Rcpp_1.1.0 scCustomize_3.2.4
[43] Seurat_5.3.0 SeuratObject_5.2.0
[45] sp_2.2-0 lubridate_1.9.4
[47] forcats_1.0.1 stringr_1.5.2
[49] dplyr_1.1.4 purrr_1.1.0
[51] readr_2.1.5 tidyr_1.3.1
[53] tibble_3.3.0 ggplot2_4.0.0
[55] tidyverse_2.0.0 DESeq2_1.46.0
[57] SummarizedExperiment_1.36.0 Biobase_2.66.0
[59] MatrixGenerics_1.18.1 matrixStats_1.5.0
[61] GenomicRanges_1.58.0 GenomeInfoDb_1.42.3
[63] IRanges_2.40.1 S4Vectors_0.44.0
[65] BiocGenerics_0.52.0 limma_3.62.2
[67] workflowr_1.7.2
loaded via a namespace (and not attached):
[1] igraph_2.1.4 ica_1.0-3
[3] Formula_1.2-5 scater_1.34.1
[5] rematch2_2.1.2 zlibbioc_1.52.0
[7] tidyselect_1.2.1 bit_4.6.0
[9] doParallel_1.0.17 BWStest_0.2.3
[11] lattice_0.22-7 rjson_0.2.23
[13] EnhancedVolcano_1.24.0 blob_1.3.0
[15] S4Arrays_1.6.0 parallel_4.4.0
[17] dichromat_2.0-0.1 png_0.1-9
[19] cli_3.6.5 ProtGenerics_1.38.0
[21] askpass_1.2.1 openssl_2.3.4
[23] goftest_1.2-3 BiocIO_1.16.0
[25] textshaping_1.0.3 glmGamPoi_1.18.0
[27] bluster_1.16.0 officer_0.7.0
[29] BiocNeighbors_2.0.1 uwot_0.2.3
[31] curl_7.0.0 mime_0.13
[33] evaluate_1.0.5 stringi_1.8.7
[35] backports_1.5.0 PMCMRplus_1.9.12
[37] XML_3.99-0.19 httpuv_1.6.16
[39] paletteer_1.7.0 magrittr_2.0.4
[41] rappdirs_0.3.4 splines_4.4.0
[43] sctransform_0.4.2 HDF5Array_1.34.0
[45] DBI_1.2.3 jquerylib_0.1.4
[47] withr_3.0.2 git2r_0.36.2
[49] reformulas_0.4.1 systemfonts_1.3.1
[51] rprojroot_2.1.1 lmtest_0.9-40
[53] tidygraph_1.3.1 rtracklayer_1.66.0
[55] BiocManager_1.30.26 htmlwidgets_1.6.4
[57] fs_1.6.6 SuppDists_1.1-9.9
[59] labeling_0.4.3 SparseArray_1.6.2
[61] truncnorm_1.0-9 reticulate_1.43.0
[63] zoo_1.8-14 XVector_0.46.0
[65] UCSC.utils_1.2.0 RhpcBLASctl_0.23-42
[67] timechange_0.3.0 foreach_1.5.2
[69] caTools_1.18.3 patchwork_1.3.2
[71] grid_4.4.0 rhdf5_2.50.2
[73] pan_1.9 RSpectra_0.16-2
[75] irlba_2.3.5.1 ggrastr_1.0.2
[77] alabaster.schemas_1.6.0 fastDummies_1.7.5
[79] lazyeval_0.2.2 yaml_2.3.10
[81] survival_3.8-3 scattermore_1.2
[83] BiocVersion_3.20.0 crayon_1.5.3
[85] RcppAnnoy_0.0.22 progressr_0.16.0
[87] tweenr_2.0.3 later_1.4.4
[89] ggridges_0.5.7 codetools_0.2-20
[91] base64enc_0.1-3 GlobalOptions_0.1.2
[93] KEGGREST_1.46.0 Rtsne_0.17
[95] shape_1.4.6.1 fastICA_1.2-7
[97] Rsamtools_2.22.0 gdtools_0.4.3
[99] filelock_1.0.3 foreign_0.8-90
[101] pkgconfig_2.0.3 xml2_1.4.0
[103] spatstat.univar_3.1-4 GenomicAlignments_1.42.0
[105] getPass_0.2-4 alabaster.base_1.6.1
[107] spatstat.sparse_3.1-0 xtable_1.8-4
[109] car_3.1-3 plyr_1.8.9
[111] httr_1.4.7 rbibutils_2.3
[113] tools_4.4.0 globals_0.18.0
[115] beeswarm_0.4.0 htmlTable_2.4.3
[117] broom_1.0.10 checkmate_2.3.3
[119] nlme_3.1-168 ExperimentHub_2.14.0
[121] crosstalk_1.2.2 lme4_1.1-37
[123] digest_0.6.37 numDeriv_2016.8-1.1
[125] bookdown_0.45 Matrix_1.7-4
[127] farver_2.1.2 tzdb_0.5.0
[129] reshape2_1.4.4 rpart_4.1.24
[131] glue_1.8.0 mice_3.18.0
[133] cachem_1.1.0 polyclip_1.10-7
[135] Hmisc_5.2-4 generics_0.1.4
[137] Biostrings_2.74.1 mvtnorm_1.3-3
[139] presto_1.0.0 parallelly_1.45.1
[141] statmod_1.5.0 impute_1.80.0
[143] RcppHNSW_0.6.0 ragg_1.5.0
[145] ScaledMatrix_1.14.0 fontBitstreamVera_0.1.1
[147] carData_3.0-5 minqa_1.2.8
[149] pbapply_1.7-4 httr2_1.2.1
[151] glmnet_4.1-10 spam_2.11-1
[153] dqrng_0.4.1 utf8_1.2.6
[155] gtools_3.9.5 graphlayouts_1.2.2
[157] alabaster.se_1.6.0 preprocessCore_1.68.0
[159] ggsignif_0.6.4 gridExtra_2.3
[161] shiny_1.11.1 GenomeInfoDbData_1.2.13
[163] rhdf5filters_1.18.1 memoise_2.0.1
[165] rmarkdown_2.30 scales_1.4.0
[167] gypsum_1.2.0 svglite_2.2.1
[169] RANN_2.6.2 fontLiberation_0.1.0
[171] spatstat.data_3.1-8 rstudioapi_0.17.1
[173] cluster_2.1.8.1 whisker_0.4.1
[175] janitor_2.2.1 spatstat.utils_3.2-0
[177] hms_1.1.4 fitdistrplus_1.2-4
[179] cowplot_1.2.0 colorspace_2.1-2
[181] rlang_1.1.7 jomo_2.7-6
[183] Rsolnp_2.0.1 DelayedMatrixStats_1.28.1
[185] sparseMatrixStats_1.18.0 dotCall64_1.2
[187] scuttle_1.16.0 ggforce_0.5.0
[189] circlize_0.4.16 mgcv_1.9-3
[191] xfun_0.53 multcompView_0.1-10
[193] alabaster.matrix_1.6.1 iterators_1.0.14
[195] abind_1.4-8 celldex_1.16.0
[197] gmp_0.7-5 Rhdf5lib_1.28.0
[199] bitops_1.0-9 Rdpack_2.6.4
[201] ps_1.9.1 promises_1.3.3
[203] RSQLite_2.4.3 DelayedArray_0.32.0
[205] Rmpfr_1.1-1 compiler_4.4.0
[207] alabaster.ranges_1.6.0 boot_1.3-32
[209] writexl_1.5.4 beachmat_2.22.0
[211] listenv_0.9.1 edgeR_4.4.2
[213] fontquiver_0.2.1 BiocSingular_1.22.0
[215] tensor_1.5.1 MASS_7.3-65
[217] kSamples_1.2-12 uuid_1.2-1
[219] BiocParallel_1.40.2 spatstat.random_3.4-2
[221] R6_2.6.1 fastmap_1.2.0
[223] rstatix_0.7.2 vipor_0.4.7
[225] ROCR_1.0-11 mcprogress_0.1.1
[227] rsvd_1.0.5 mitml_0.4-5
[229] nnet_7.3-20 gtable_0.3.6
[231] KernSmooth_2.23-26 miniUI_0.1.2
[233] deldir_2.0-4 htmltools_0.5.8.1
[235] bit64_4.6.0-1 spatstat.explore_3.5-3
[237] lifecycle_1.0.5 ggprism_1.0.7
[239] HardyWeinberg_1.7.9 S7_0.2.0
[241] zip_2.3.3 processx_3.8.6
[243] restfulr_0.0.16 nloptr_2.2.1
[245] callr_3.7.6 sass_0.4.10
[247] vctrs_0.7.1 isoband_0.2.7
[249] flextable_0.9.10 spatstat.geom_3.6-0
[251] snakecase_0.11.1 scran_1.34.0
[253] future.apply_1.20.0 bslib_0.9.0
[255] pillar_1.11.1 gplots_3.2.0
[257] rmdformats_1.0.4 metapod_1.14.0
[259] combinat_0.0-8 locfit_1.5-9.12
[261] jsonlite_2.0.0 chron_2.3-62