This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Possible downsides for direct gene list analysis in Gene Ontology?

Hi all,

As a follow-up of this post, I am tempted to provide a list of genes (with no numeric values) to the http://www.pantherdb.org/ for statistical overrepresentation test.

  1. Any downside of taking this route?
  2. As far as I know, I can provide a list of genes with numeric values for statistical enrichment test. Is it better than overrepresentation test? If so, what kind of numerical values should I provide from DESeq2 output?
  3. In terms of providing "better" results (not just the convenience of using R), should I use other R packages for gene ontology analysis? For example, GOseq?

Thanks!

rna-seq gene ontology goseq r panther
• 2,711 views • link
updated by Biostar Biostar • written by CandiceChuDVM CandiceChuDVM

Were the gene lists split into up-/down- regulated for the submission?

• 1 views • link
written by GenoMax GenoMax

I use goseq for results from RNA-seq studies. It's similar as enrichment analysis, but it takes a length bias into account.

You don't need any values, only a list of significant genes (and a list of all genes in your experiment).

• 1 views • link
written by Benn Benn

Hi b.nota,

By "a list of all genes in your experiment", do you mean "reference genome of the species used in the experiment"? I always use reference genome as my background without thinking. Maybe I should use "a list of all genes in your experiment" instead.

• 1 views • link
written by CandiceChuDVM CandiceChuDVM

Hi, sorry for the late reply...

Yes, all genes from reference can be used. But alternatively you can also use all genes that are left after filtering in e.g., edgeR. Usually you filter out genes first, with no or low number of reads before differential analysis.

• 0 views • link
written by Benn Benn

0 answers

No answers yet.

Log in to answer this question.

More posts like this