Question: no significant FDR in gene enrichment analysis
gravatar for nazaninhoseinkhan
2.4 years ago by
Iran, Islamic Republic Of
nazaninhoseinkhan410 wrote:

Dear all,

I have a large list of DEGs (around 400). However when I tried to do pathway enrichment analysis using DAVID, PANTHER or Enrichr, based on FDR only 1 pathway was detected.

Can u tell me the probable reason for this? Is there anything that I did not consider?

Looking forward to your comments

Nazanin Hosseinkhan

rna-seq degs enrichment fdr • 999 views
ADD COMMENTlink written 2.4 years ago by nazaninhoseinkhan410

Please give information on the experimental setup, the number of samples, treatment and the tool that was used for differential analysis.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by ATpoint42k

52 tumor samples vs 3 normal tissues belong to TCGA project were compared using DESeq2 program.

ADD REPLYlink written 2.4 years ago by nazaninhoseinkhan410

The comparison is imbalanced - which TCGA dataset is it? Are you using FPKM data? FPKM data is not suitable for cross-sample differential expression analysis. From where did you obtain the data?

ADD REPLYlink written 2.3 years ago by Kevin Blighe68k

Hi Kevin,

I imported a list of deregulated genes( 30 down vs. 48 up-regulated) resulted from DESEq2 into Enrichr. However, no FDR significant pathways were detected. I checked some of my genes in KEGG and strangely they were detected in the same pathways. I could not understand the meaning of FDR in this context, i.e. pathway enrichment. Could you please explain to me why no pathway has significant FDR in Enrichr.

Thank you in advance Nazanin

ADD REPLYlink written 2.3 years ago by nazaninhoseinkhan410

I see. 30 + 48 genes is not that much for gene enrichment or pathway analysis, which is probably why you are not obtaining any significant adjusted P values. With that small number of genes, have you tried to just do a literature search to infer (yourself) in which pathways these genes belong?

ADD REPLYlink written 2.3 years ago by Kevin Blighe68k

Enrichr identified the same pathways as KEGG. I manually searched some of my genes by KEGG. So is it correct if I ignore the FDRs reported by Enrichr?

ADD REPLYlink written 2.3 years ago by nazaninhoseinkhan410

You can choose to ignore them, if you wish, but you should report some enrichment score and/or unadjusted P value. If you publish the data, you may be questioned by a reviewer / asked for clarification on why you did not use the adjusted P values.

I still believe that a full day of literature searching involving your gene of interest would be more productive. You only have 78.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Kevin Blighe68k


I will literature searching them. If I understood correctly, the KEGG has not been updated since 2016 and if I do literature searching I might found more pathways than KEGG.

Thank you again for your prompt response

ADD REPLYlink written 2.3 years ago by nazaninhoseinkhan410
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