Question: MUC5AC is not present in deseq2 results
0
gravatar for nazaninhoseinkhan
8 weeks ago by
Iran, Islamic Republic Of
nazaninhoseinkhan400 wrote:

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

rna-seq deseq2 muc5ac • 140 views
ADD COMMENTlink written 8 weeks ago by nazaninhoseinkhan400
1

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.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by ATpoint34k

@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.

ADD REPLYlink written 8 weeks ago by Haci370

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.

ADD REPLYlink written 8 weeks ago by nazaninhoseinkhan400

Thanks for your comment.

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

ADD REPLYlink written 8 weeks ago by nazaninhoseinkhan400

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.

ADD REPLYlink written 8 weeks ago by ATpoint34k

It is not present in the htseq count files

ADD REPLYlink written 8 weeks ago by nazaninhoseinkhan400
2
gravatar for Haci
8 weeks ago by
Haci370
Haci370 wrote:

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

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by Haci370

Yes, probably this is the case.

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

ADD REPLYlink written 8 weeks ago by nazaninhoseinkhan400

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?

ADD REPLYlink written 8 weeks ago by Haci370

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

ADD REPLYlink written 8 weeks ago by nazaninhoseinkhan400

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?

ADD REPLYlink written 8 weeks ago by ATpoint34k

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

ADD REPLYlink written 8 weeks ago by nazaninhoseinkhan400
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