Last updated: 2024-09-25
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Knit directory: lung_lymph_scMultiomics/
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File | Version | Author | Date | Message |
---|---|---|---|---|
Rmd | 576130e | Jing Gu | 2024-09-25 | corrected GO database |
html | f649cf3 | Jing Gu | 2024-09-19 | Build site. |
Rmd | 1e7e576 | Jing Gu | 2024-09-19 | look into k5 genes with high z scores |
html | 9b3d3f3 | Jing Gu | 2024-09-11 | Build site. |
Rmd | be37d0b | Jing Gu | 2024-09-11 | plotted heatmaps for enrichment results |
html | c596528 | Jing Gu | 2024-09-11 | Build site. |
Rmd | 3d34658 | Jing Gu | 2024-09-11 | plotted heatmaps for enrichment results |
html | ede96e9 | Jing Gu | 2024-09-11 | Build site. |
Rmd | 163b422 | Jing Gu | 2024-09-11 | plotted heatmaps for enrichment results |
html | 87c183b | Jing Gu | 2024-05-25 | Build site. |
Rmd | b7a8317 | Jing Gu | 2024-05-25 | updated result page |
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Rmd | 36aceab | Jing Gu | 2024-05-23 | organized results |
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Rmd | 5c6b22f | Jing Gu | 2024-05-22 | updated GSEA results |
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Rmd | 3e4f015 | Jing Gu | 2024-05-13 | wflow_publish("analysis/cross_tissue_DE_u19_fastTopics.Rmd") |
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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 |
Parameters:
N_updates = 150 N_topics = 12
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-02
Set 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 |
plot by tissue
plot by tissue and cell-type
Two ways to perform enrichment test:
A test purely depends on occurrences, asking whether the genes related to a topic occur more frequently in GO term compared to the background genes.
It tests whether the genes in a set is more associated with phenotype than those outside of a set.
Input:
Top loading genes are enriched in large number of GO terms, which have broad functions.
gene-set inputs: top 100 genes from each topic + immune cell markers GWAS: ukb-a-446
Input:
Volcano plots for GoM DE results
Axis: the z-scores for posterior mean log-fold change estimates vs. log-fold change
From volcano plots, we see several genes that encode different types of cytokines are present in topic 6. Chemokine ligands (CCL4, CCL20, etc.) are proteins that signal leukocyte migration, while cytokines (IL17A, IL22) are interleukins that signal immune cells to defend against pathogens.
[1] "Number of up-regulated genes in each topic against the rest:"
t1 t2 t3 t4 t5 t6 t7 t8 t9 t10 t11 t12
1602 122 594 562 391 381 267 505 111 626 465 489
GO Enrichment result table
All topics have fewer number of GO terms with enrichment, except for topic 1.
Visualizing GO enrichment with ComplexHeatmap
Parameters:
Legend:
BP results show k1 enriched for granulocyte activation and neutrophil mediated immunity, as well as cell adhesion and motility. These pathways are highly relevant to Asthma. Due to high number of GO terms over-represented by k1 genes, we may repeat the topic modeling by increasing topic number. Several topics like k2, 6, 7, 9, 10 are strongly enriched with protein localization. Topics k3-6 have genes over-represented in T-cell activation, while k10, 12 in B-cell activation.
MF results show broad enrichment of molecular binding, with k7 highly enriched for cell adhesion molecular binding.
Selecting by FDR
Version | Author | Date |
---|---|---|
f649cf3 | Jing Gu | 2024-09-19 |