MUC5AC is not present in deseq2 results

Question

[nazaninhoseinkhan]

Dear all,

I am working on a RNASeq data set of Gastric Cancer.

However after running Deseq2, The gene MUC5AC which is one the most important genes in this malignancy is not present among 23367 genes.

I also checked for MUC5AC synonyms, but I could not find it.

I used hg19 gtf for this analysis.

I will appreciate any comments

Nazanin

[ATpoint]

It is probably filtered-out by the independent filtering when running results. Try to turn it off with independentFiltering=FALSE. Also be sure that it is indeed present in the input count matrix but you probably checked that already.

[Haci]

@ATpoint, do you think it is likely that a key gene in some malignancy is lost after independent filtering?

@nazaninhoseinkhan, I would double check if your gene of interest is really present in your genome annotation file. There are major and minor versions, for example, MUC2, another mucine gene, is present in GRCh38.93.gtf but not in GRCh38.84.gtf.

[nazaninhoseinkhan]

I used hg19 (GRCH37) gtf file for annotation.

I carried out this analysis for a team working on Gastric Cancer.

They told me that they wanted to check the expression of MUC5AC.

All other Mucins are present in deseq2 output but not for MUC5AC.

[nazaninhoseinkhan]

Thanks for your comment.

I turned off "independentFiltering=FALSE", but nothing changed. The number of genes was again 23367.

[ATpoint]

Also be sure that it is indeed present in the input count matrix but you probably checked that already.

Please do this. Be sure the gene is present in the input.

[nazaninhoseinkhan]

It is not present in the htseq count files

Answer 1

[Haci]

Probably because it is not in the gtf file you used, hence my previous comment.

[nazaninhoseinkhan]

Yes, probably this is the case.

However I do not understand why this important gene is not present in hg19 gtf file.

[Haci]

I have no idea but I think it's worth being asked as a separate question. But did you confirm that it is really not in your annotation file?

[nazaninhoseinkhan]

Yes, I checked hg19 gtf for the name "MUC5AC" or "NM_001304359" and unfortunately it was not present there.

[ATpoint]

Ok, so not a DESeq2 issue at all. Did you manually search for the gene like extracting the coordinate range where it is supposed to be from the GTF file and then check if it maybe has an unexpected name in the file you use?

[nazaninhoseinkhan]

Yes,I searched manually for "MUC5AC", "NM_001304359" and for its coordinate (1157953-1201138), but no one was present.