bio-workflows-expression-to-pathways

Version Compatibility

Reference examples tested with: DESeq2 1.42+, R stats (base), ReactomePA 1.46+, clusterProfiler 4.10+, ggplot2 3.5+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Expression to Pathways Workflow

"Find enriched pathways from my differential expression results" → Orchestrate GO enrichment (clusterProfiler), GSEA, KEGG/Reactome pathway mapping, and enrichment visualization from DE gene lists or ranked gene lists.

Convert differential expression results into biological insights through functional enrichment analysis.

Workflow Overview

DE Results (gene list or ranked list)
    |
    v
[1. Gene ID Conversion] --> Convert to Entrez/Ensembl
    |
    v
[2. Over-representation Analysis]
    |
    +---> GO Enrichment (BP, MF, CC)
    |
    +---> KEGG Pathways
    |
    +---> Reactome Pathways
    |
    v
[3. GSEA (ranked genes)]
    |
    v
[4. Visualization] -----> Dot plots, networks, bar plots
    |
    v
Functional annotations and pathway insights

Input Preparation

From DESeq2 Results

library(DESeq2)
library(clusterProfiler)
library(org.Hs.eg.db)

# Load DE results
res <- read.csv('deseq2_results.csv', row.names = 1)

# Significant genes for ORA
sig_genes <- rownames(subset(res, padj < 0.05 & abs(log2FoldChange) > 1))

# All genes for background
all_genes <- rownames(res)

# Ranked list for GSEA (by stat or log2FC)
ranked_genes <- res$log2FoldChange
names(ranked_genes) <- rownames(res)
ranked_genes <- sort(ranked_genes, decreasing = TRUE)
ranked_genes <- ranked_genes[!is.na(ranked_genes)]

Gene ID Conversion

# Convert gene symbols to Entrez IDs
sig_entrez <- bitr(sig_genes, fromType = 'SYMBOL', toType = 'ENTREZID',
                   OrgDb = org.Hs.eg.db)

# For ranked list
ranked_entrez <- bitr(names(ranked_genes), fromType = 'SYMBOL', toType = 'ENTREZID',
                      OrgDb = org.Hs.eg.db)
ranked_list <- ranked_genes[ranked_entrez$SYMBOL]
names(ranked_list) <- ranked_entrez$ENTREZID