Deleted:How to analyze gene regulatory networks from existing DE gene expression results, Reactome pathways and TFs?
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21 days ago
jay • 0

I want to analyze how differential expressed (DE) genes in Reactome pathways (R-HSAs) are connected to active transcription factors (TF) to identify potential co-regulation and better understand the role of TFs in the R-HSAs. I believe this is called gene regulatory network (GRN) analysis. With the results I want to construct and visualize a network diagram showing the genes/TFs as nodes clustered according to the R-HSAs and their connections as edges. However, I have to continue working with the results of an already completed DE gene analysis because the computation was done in a complicated way, using sampling weights.

What I have:

  • human TMM-normalized mRNA-seq data from blood
  • DE gene analysis, log2FC as well as p.adj available in a result matrix for each ENSEMBL gene (~17K, ~1K DE)
  • from DE genes I obtained some up- and downregulated functional R-HSAs and 27 active TFs (and TF:TF interactions) using gprofiler2::gost

Challenges faced:

  • I manually created overlaps between the active TFs and the DE genes of the individual R-HSAs, which was insightful, but of course it doesn't give me any stats.

  • Following biostars answers, I have tried a number of packages, such as WGCNA, MOFA2, and CeTF, but 1. they do not correspond to the intention of the analysis and 2. they can't include pre-analyzed DE gene data with sampling weights.

  • Then I tried RTN, which looks promising, but I'm not sure how to use the R-HSAs in it. I also tried SBGNview on the R-HSAs, which looks beautiful, but I'm not sure how to 1. combine more R-HSAs in one plot with co-expressed genes connected, or 2. show TFs there.

Seeking advice on:

  1. tools or methods that can integrate my existing DE genes, R-HSAs, and TF data for detailed GRN analysis
  2. strategies for creating/visualizing a network that highlights TFs co-regulating the R-HSAs
  3. good example studies that have done something similar
r transcription-factor regulatory-network rna-seq reactome • 163 views
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