SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
duplicate reads still present after MarkDuplicates Morgane_AUS Bioinformatics 9 09-22-2014 09:41 AM
I present myself camilla_87 Introductions 0 09-17-2014 02:18 AM
Stacks exce_velvetg not present bio_jit Bioinformatics 0 07-02-2014 09:43 PM
Enrichment with AGILENT's Sureselect target enrichment system dottomarco 454 Pyrosequencing 1 11-18-2009 01:14 AM
Poor enrichment...defective enrichment beads? njae4 454 Pyrosequencing 0 03-09-2009 06:23 AM

Reply
 
Thread Tools
Old 05-06-2015, 05:31 AM   #1
likebiology
Member
 
Location: haifa, Israel

Join Date: Aug 2013
Posts: 14
Default how to filter the same GO present in both up- and down-regulated GO enrichment

Hi all,

I compared two groups of transcriptomes, up- and down-regulated genes were isolated. GO enrichment was carried out on these differential expressed genes. But some GO terms are present in both groups, I think it is conflict, Could anybody explain to me is it reasonable? If not, how to filter it? Thank you!

Best regards,
likebiology is offline   Reply With Quote
Old 05-08-2015, 07:54 AM   #2
mbblack
Senior Member
 
Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245
Default

You mean the same GO terms in both the up-regulated and the down-regulated group? If so, sure that's highly possible. Remember that individual gene differential expression does not necessarily tell you the overall affect on a complete biochemical process or pathway. So it is very possible to have conflicting changes in separate genes in a given pathway.

All enrichment tells you is which pathways included gene products from your differentially expressed genes beyond what would be predicted by chance overlap alone. It does not tell you anything about the direction nor magnitude of change in the output of a pathway.
__________________
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.

Last edited by mbblack; 05-08-2015 at 07:56 AM.
mbblack is offline   Reply With Quote
Old 05-08-2015, 08:42 AM   #3
likebiology
Member
 
Location: haifa, Israel

Join Date: Aug 2013
Posts: 14
Default

Thank you Michael for your kind reply!

You are right. the same GO term is present in both up- and down- regulated group. I checked the genes in such GO terms and I found some of the genes are the same. So I think may be because of isoforms or bad assembly (de novo).If so, what do you suggest to do?

Thank you!

Best,
likebiology is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:55 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO