Question: Geneset enrichment in non-model organism with DAVID
0
gravatar for pbigbig
3.9 years ago by
pbigbig200
United States
pbigbig200 wrote:

Hi everyone,

I have an assembled whole transcriptome and several transcriptomes from different development stage of a non-model fish. Basically, I would like to see which gene, gene groups and/or pathways is specifically expressed in which development stage, so there are differential expression analysis and gene enrichment analysis need to be performed.

I wonder if this is a correct way that I use only orthologs of my fish vs zebrafish (given that they are closely related in taxonomical term) and then use genelist based on zebrafish hits for geneset enrichment analysis on DAVID? Is there another feasible approach for this kind of analysis on non-model organism? Any advice and suggestion are greatly welcomed

Thank you very much!

Phuong

geneset enrichment david • 1.5k views
ADD COMMENTlink modified 3.9 years ago by Pappu1.9k • written 3.9 years ago by pbigbig200

maybe you can use clusterProfiler.

ADD REPLYlink written 3.9 years ago by Guangchuang Yu2.3k

Thanks for your suggestion!

ADD REPLYlink written 3.9 years ago by pbigbig200
0
gravatar for Pappu
3.9 years ago by
Pappu1.9k
Pappu1.9k wrote:

You can try GSEA of Broad.

ADD COMMENTlink written 3.9 years ago by Pappu1.9k

Thanks for your suggestion!

ADD REPLYlink written 3.9 years ago by pbigbig200
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 825 users visited in the last hour