cross-tissue DE analysis with fastTopics
Jing Gu
2024-04-29
Last updated: 2024-05-22
Checks: 7 0
Knit directory: lung_lymph_scMultiomics/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 5c6b22f | Jing Gu | 2024-05-22 | updated GSEA results |
| html | 3d73252 | Jing Gu | 2024-05-13 | Build site. |
| Rmd | f26e8ad | Jing Gu | 2024-05-13 | wflow_publish("analysis/cross_tissue_DE_u19_fastTopics.Rmd") |
| html | 95bfdff | Jing Gu | 2024-05-13 | Build site. |
| Rmd | 3e4f015 | Jing Gu | 2024-05-13 | wflow_publish("analysis/cross_tissue_DE_u19_fastTopics.Rmd") |
| html | 2e475c9 | Jing Gu | 2024-05-13 | Build site. |
| Rmd | 306ddb1 | Jing Gu | 2024-05-13 | wflow_publish("analysis/cross_tissue_DE_u19_fastTopics.Rmd") |
| html | f812a40 | Jing Gu | 2024-05-09 | Build site. |
| html | 68d9e18 | Jing Gu | 2024-05-09 | Build site. |
| Rmd | 7ca45f6 | Jing Gu | 2024-05-09 | cross-tissue comparison |
| Rmd | 7a45261 | Jing Gu | 2024-05-08 | cross-tissue comparison with topic modeling |
GoM DE analysis on u19 dataset
Model fitting
Parameters:
N_updates = 150 N_topics = 12
Model evaluation
check the convergence
| Version | Author | Date |
|---|---|---|
| 68d9e18 | Jing Gu | 2024-05-09 |
Model overview:
Number of data rows, n: 53647
Number of data cols, m: 17420
Rank/number of topics, k: 12
Evaluation of model fit (170 updates performed):
Poisson NMF log-likelihood: -1.997995557900e+08
Multinomial topic model log-likelihood: -1.995509032083e+08
Poisson NMF deviance: +2.634951598369e+08
Max KKT residual: +1.430262e-02Set show.size.factors = TRUE, show.mixprops = TRUE and/or show.topic.reps = TRUE in print(...) for more information
| Version | Author | Date |
|---|---|---|
| 68d9e18 | Jing Gu | 2024-05-09 |
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.
| Version | Author | Date |
|---|---|---|
| 68d9e18 | Jing Gu | 2024-05-09 |
Visualize topics with structural plots
- plot by cell-types
| Version | Author | Date |
|---|---|---|
| 68d9e18 | Jing Gu | 2024-05-09 |
- plot by tissue
| Version | Author | Date |
|---|---|---|
| 68d9e18 | Jing Gu | 2024-05-09 |
- plot by tissue and cell-type
| Version | Author | Date |
|---|---|---|
| 68d9e18 | Jing Gu | 2024-05-09 |
Validate topics with enrichment test
GO enrichemnt test on top 500 genes ranked by loadings
GO enrichemnt test on GoM DE analysis
Volcano plots for GoM DE results
The z-scores for posterior mean log-fold change estimates
vs. log-fold change
| Version | Author | Date |
|---|---|---|
| 2e475c9 | Jing Gu | 2024-05-13 |
| Version | Author | Date |
|---|---|---|
| 2e475c9 | Jing Gu | 2024-05-13 |
| Version | Author | Date |
|---|---|---|
| 2e475c9 | Jing Gu | 2024-05-13 |
GO Enrichemnt results for upregulated genes with local false sign rates < 0.01
Topic 3,4,5,6 show strong enrichment for the GO terms of T-cell activation, leukocyte differentiation, positive regulation of cell adhesion, adaptive immune response.
From volcano plots, we see topic 6 has high LFC in genes such as IL17A, IL22, which are mainly produced by Th17 cells.
Topic 11 is strongly enriched for GO terms related to regulation of innate or adaptive immune response.
Topic 12 shows strong enrichment for the GO term of B cell activation.
Identify topics correlated with differences between tissue
- test whether any topic is associated with transcriptional differences across tissue \[ L = \beta X_{\text{tissue}} + \text{Covariates} + \epsilon \]
- perform T-test to see whether topic proportions between two tissues are significantly different
Density plot for topic proportions between tissue across cell types
X-axis denotes the percentage format of topic proportion.
Y-axis represents the density of cells with respect to topic
proportions.
Topic 1 is specific to cell types other than lymphocytes.
Topic 3 is highly represented in NK and \(CD8^+\) T cells.
Topic 4-5 are T-cell specific, with clear separation between tissue in \(CD8^+\) T for topic 4 and Treg for topic 5.
Topic 6 is specific to Th17 cells and lungs has a longer tail of distribution compared to spleens.
Topic 2,7,8,9 show similar distributions across cell types without clear separation between tissue.
Topic 10-12 show higher density in B cells. Topic 11 captures tissue difference mainly in Memory B cells, while topic 12 displays some separation between tissue in Naive B cells.
Barplot for topic proportions in cell types
- The topic proportion for k10 is higher in spleens than lungs in both naive B and memory B cells.
- The topic proportions for k11 is higher in spleens than lungs in memory B cells only.
- The topic proportions for k4 is higher in spleens than lungs across cell types.
- The topic proportions for k6 is higher in lungs than spleens across cell types.
- The topic proportions for k5 is higher in lungs than spleens across T cell subsets.
NK other Memory_B Naive_B Treg CD4_T CD8_T Th17
lungs 8067 1654 5287 1174 1336 6980 12210 2732
spleens 464 104 10507 1710 47 886 421 68`summarise()` has grouped output by 'tissue', 'celltype'. You can override
using the `.groups` argument.# A tibble: 192 × 4
# Groups: tissue, celltype [16]
tissue celltype topic topic_prop_sum
<chr> <fct> <chr> <dbl>
1 lungs NK k1 56.9
2 lungs NK k10 17.8
3 lungs NK k11 70.0
4 lungs NK k12 30.6
5 lungs NK k2 555.
6 lungs NK k3 3886.
7 lungs NK k4 314.
8 lungs NK k5 695.
9 lungs NK k6 613.
10 lungs NK k7 681.
# ℹ 182 more rows`summarise()` has grouped output by 'tissue', 'celltype'. You can override
using the `.groups` argument.
`summarise()` has grouped output by 'tissue', 'celltype'. You can override
using the `.groups` argument.
All k4 terms included in k5.
k
1 k5
2 k5
3 k5
4 k5
5 k5
6 k5
7 k5
8 k5
9 k5
10 k5
11 k5
12 k5
13 k5
14 k5
15 k5
16 k5
17 k5
18 k5
19 k5
20 k5
21 k5
22 k5
23 k5
24 k5
25 k5
26 k5
27 k5
28 k5
29 k5
30 k5
31 k5
32 k5
33 k5
34 k5
35 k5
36 k5
37 k5
38 k5
39 k5
40 k5
41 k5
42 k5
43 k5
44 k5
45 k5
46 k5
47 k5
48 k5
49 k5
50 k5
51 k5
52 k5
53 k5
54 k5
55 k5
56 k5
57 k5
58 k5
59 k5
description
1 immune response-regulating signaling pathway
2 stress-activated protein kinase signaling cascade
3 intracellular receptor signaling pathway
4 covalent chromatin modification
5 regulation of hemopoiesis
6 protein modification by small protein removal
7 peptidyl-serine modification
8 response to tumor necrosis factor
9 activation of protein kinase activity
10 regulation of multi-organism process
11 regulation of innate immune response
12 cellular response to environmental stimulus
13 homeostasis of number of cells
14 positive regulation of cellular protein localization
15 regulation of apoptotic signaling pathway
16 myeloid cell differentiation
17 fat cell differentiation
18 peptidyl-lysine modification
19 regulation of mRNA metabolic process
20 regulation of protein serine/threonine kinase activity
21 coagulation
22 posttranscriptional regulation of gene expression
23 face development
24 negative regulation of catabolic process
25 regulation of protein modification by small protein conjugation or removal
26 viral life cycle
27 vascular endothelial growth factor receptor signaling pathway
28 cell-cell signaling by wnt
29 response to virus
30 regulation of protein localization to membrane
31 hormone-mediated signaling pathway
32 positive regulation of defense response
33 positive regulation of cytokine production
34 establishment or maintenance of cell polarity
35 epithelial cell apoptotic process
36 response to peptide
37 I-kappaB kinase/NF-kappaB signaling
38 positive regulation of proteolysis
39 ERBB signaling pathway
40 endomembrane system organization
41 phagocytosis
42 extrinsic apoptotic signaling pathway
43 regulation of body fluid levels
44 Ras protein signal transduction
45 platelet morphogenesis
46 regulation of small GTPase mediated signal transduction
47 regulation of gene expression, epigenetic
48 type I interferon production
49 response to mechanical stimulus
50 interaction with host
51 protein localization to mitochondrion
52 ERK1 and ERK2 cascade
53 positive regulation of catabolic process
54 positive regulation of establishment of protein localization
55 maintenance of cell number
56 neuron migration
57 cellular response to external stimulus
58 nuclear transport
59 regulation of cell cycle phase transition
FDR
1 3.492289e-06
2 9.634677e-06
3 2.410475e-05
4 2.015496e-04
5 1.122854e-03
6 1.122854e-03
7 1.122854e-03
8 1.122854e-03
9 1.122854e-03
10 1.599627e-03
11 1.691464e-03
12 2.125044e-03
13 2.125044e-03
14 2.125044e-03
15 2.749721e-03
16 2.749721e-03
17 2.749721e-03
18 2.749721e-03
19 3.516024e-03
20 3.516024e-03
21 3.839176e-03
22 5.894825e-03
23 5.894825e-03
24 6.999863e-03
25 6.999863e-03
26 8.081150e-03
27 9.224868e-03
28 1.097745e-02
29 1.216695e-02
30 1.231576e-02
31 1.334113e-02
32 1.344643e-02
33 1.344936e-02
34 1.344936e-02
35 1.437995e-02
36 1.437995e-02
37 1.502224e-02
38 1.502224e-02
39 1.582629e-02
40 1.582629e-02
41 1.601051e-02
42 1.958226e-02
43 2.037542e-02
44 2.457071e-02
45 2.685611e-02
46 2.685611e-02
47 2.823422e-02
48 2.966939e-02
49 2.974703e-02
50 2.974703e-02
51 3.236806e-02
52 3.383944e-02
53 3.664705e-02
54 3.939417e-02
55 4.209289e-02
56 4.326526e-02
57 4.326526e-02
58 4.798100e-02
59 4.911061e-02 description
1 immune response-regulating signaling pathway
2 stress-activated protein kinase signaling cascade
3 intracellular receptor signaling pathway
4 covalent chromatin modification
5 peptidyl-serine modification
6 activation of protein kinase activity k description FDR
1 k6 RNA catabolic process 0.000000e+00
2 k6 establishment of protein localization to membrane 0.000000e+00
3 k6 translational initiation 0.000000e+00
4 k6 protein localization to endoplasmic reticulum 0.000000e+00
5 k6 protein targeting 8.179679e-12
6 k6 cytoplasmic translation 2.553424e-06
7 k6 cell chemotaxis 1.309663e-04
8 k6 adaptive immune response 2.404495e-04
9 k6 cell killing 2.404495e-04
10 k6 regulation of immune effector process 3.429156e-04
11 k6 regulation of inflammatory response 4.284072e-04
12 k6 response to toxic substance 9.748643e-04
13 k6 defense response to other organism 9.904442e-04
14 k6 lymphocyte mediated immunity 1.241181e-03
15 k6 rRNA metabolic process 1.241181e-03
16 k6 negative regulation of cytokine production 3.300686e-03
17 k6 regulation of binding 3.796800e-03
18 k6 negative regulation of transferase activity 4.316427e-03
19 k6 positive regulation of cell motility 4.343224e-03
20 k6 response to molecule of bacterial origin 4.451778e-03
21 k6 response to interleukin-1 4.584415e-03
22 k6 reactive oxygen species metabolic process 5.205687e-03
23 k6 leukocyte migration 6.552090e-03
24 k6 response to interferon-gamma 1.182491e-02
25 k6 negative regulation of immune system process 1.215541e-02
26 k6 response to type I interferon 1.215541e-02
27 k6 negative regulation of transport 1.372321e-02
28 k6 positive regulation of ion transport 1.432155e-02
29 k6 interleukin-2 production 1.518603e-02
30 k6 maintenance of location 1.550851e-02
31 k6 response to interferon-beta 1.551577e-02
32 k6 cellular response to inorganic substance 1.605400e-02
33 k6 ribonucleoprotein complex biogenesis 2.164148e-02
34 k6 response to metal ion 2.299810e-02
35 k6 lymphocyte activation involved in immune response 2.307944e-02
36 k6 tumor necrosis factor superfamily cytokine production 2.324505e-02
37 k6 cellular response to biotic stimulus 2.414756e-02
38 k6 cytolysis 2.422372e-02
39 k6 leukocyte proliferation 2.586724e-02
40 k6 interleukin-12 production 2.601286e-02
41 k6 negative regulation of growth 2.910712e-02
42 k6 regulation of DNA-binding transcription factor activity 3.470785e-02
43 k6 regulation of metal ion transport 4.227634e-02
44 k6 tolerance induction 4.227634e-02
45 k6 interferon-gamma production 4.228501e-02
46 k6 positive regulation of response to external stimulus 4.614297e-02
47 k6 positive chemotaxis 4.731393e-02All k10 terms included in k11.
k description FDR
1 k11 immune response-regulating signaling pathway 0.0002769325
2 k11 RNA catabolic process 0.0008400905
3 k11 translational initiation 0.0009933375
4 k11 protein modification by small protein removal 0.0026623734
5 k11 adaptive immune response 0.0105244395
6 k11 intrinsic apoptotic signaling pathway 0.0105244395
7 k11 regulation of mRNA metabolic process 0.0115369438
8 k11 covalent chromatin modification 0.0182460356
9 k11 cytoplasmic translation 0.0281927311
10 k11 stress-activated protein kinase signaling cascade 0.0323421456
11 k11 regulation of innate immune response 0.0405294541
12 k11 regulation of protein stability 0.0405294541
13 k11 ribonucleoprotein complex subunit organization 0.0405294541
14 k11 establishment of protein localization to membrane 0.0414053094
15 k11 ribonucleoprotein complex biogenesis 0.0414053094
16 k11 posttranscriptional regulation of gene expression 0.0414107071
17 k11 interaction with host 0.0456587986
18 k11 leukocyte cell-cell adhesion 0.0456587986
19 k11 regulation of DNA-binding transcription factor activity 0.0468421506
20 k11 cellular response to biotic stimulus 0.0483566047Perform t-test while adjusting for confounders
Procedure
Test mean difference between tissue one donor at a time and then do meta-analysis with Fisher’s method
Results
X-axis denotes cell types and y-axis denotes the topics. For major cell types, we saw majority of topics have significant differences in proportions between tissue.
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C
[4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ComplexHeatmap_2.14.0 colorRamp2_0.1.0 tidyr_1.3.1
[4] dplyr_1.1.4 poolr_1.1-1 cowplot_1.1.3
[7] ggplot2_3.5.1 fastTopics_0.6-175 Matrix_1.6-5
[10] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] matrixStats_1.2.0 fs_1.6.4 RColorBrewer_1.1-3
[4] doParallel_1.0.17 progress_1.2.3 httr_1.4.7
[7] rprojroot_2.0.4 tools_4.2.0 bslib_0.7.0
[10] DT_0.33 utf8_1.2.4 R6_2.5.1
[13] irlba_2.3.5.1 BiocGenerics_0.44.0 uwot_0.2.2
[16] lazyeval_0.2.2 colorspace_2.1-0 GetoptLong_1.0.5
[19] withr_3.0.0 tidyselect_1.2.1 prettyunits_1.2.0
[22] processx_3.8.3 compiler_4.2.0 git2r_0.33.0
[25] cli_3.6.2 Cairo_1.6-2 plotly_4.10.4
[28] labeling_0.4.3 sass_0.4.9 scales_1.3.0
[31] SQUAREM_2021.1 quadprog_1.5-8 callr_3.7.3
[34] pbapply_1.7-2 mixsqp_0.3-54 stringr_1.5.1
[37] digest_0.6.35 rmarkdown_2.26 RhpcBLASctl_0.23-42
[40] pkgconfig_2.0.3 htmltools_0.5.8.1 highr_0.10
[43] fastmap_1.1.1 invgamma_1.1 GlobalOptions_0.1.2
[46] htmlwidgets_1.6.4 rlang_1.1.3 rstudioapi_0.15.0
[49] farver_2.1.1 shape_1.4.6 jquerylib_0.1.4
[52] generics_0.1.3 jsonlite_1.8.8 crosstalk_1.2.1
[55] gtools_3.9.5 magrittr_2.0.3 S4Vectors_0.36.2
[58] Rcpp_1.0.12 munsell_0.5.1 fansi_1.0.6
[61] lifecycle_1.0.4 stringi_1.7.6 whisker_0.4.1
[64] yaml_2.3.8 mathjaxr_1.6-0 Rtsne_0.17
[67] parallel_4.2.0 promises_1.3.0 ggrepel_0.9.5
[70] crayon_1.5.2 lattice_0.22-5 circlize_0.4.15
[73] hms_1.1.3 knitr_1.46 ps_1.7.6
[76] pillar_1.9.0 rjson_0.2.21 stats4_4.2.0
[79] codetools_0.2-19 glue_1.7.0 evaluate_0.23
[82] getPass_0.2-2 data.table_1.15.4 RcppParallel_5.1.7
[85] vctrs_0.6.5 png_0.1-8 httpuv_1.6.14
[88] foreach_1.5.2 gtable_0.3.5 purrr_1.0.2
[91] clue_0.3-65 ashr_2.2-63 cachem_1.0.8
[94] xfun_0.43 later_1.3.2 viridisLite_0.4.2
[97] truncnorm_1.0-9 tibble_3.2.1 iterators_1.0.14
[100] IRanges_2.32.0 cluster_2.1.6