SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-seq remove any reads that map more than 2 times. fabrice Bioinformatics 3 08-17-2011 03:06 AM
ChIP-Seq: EpiChIP: gene-by-gene quantification of epigenetic modification levels. Newsbot! Literature Watch 0 12-07-2010 03:00 AM
How is SNP quality calculated in SAMTOOLS pileup? lazyworm Bioinformatics 2 05-28-2010 01:00 AM
RPKM as calculated by TopHat rpm16 Bioinformatics 1 10-21-2009 09:27 AM
Corona Lite Running Times? doxologist SOLiD 24 04-21-2009 10:27 PM

Reply
 
Thread Tools
Old 02-08-2010, 06:15 AM   #1
zslee
Member
 
Location: shanghai of china

Join Date: May 2009
Posts: 29
Default about David, why one gene is calculated 3 times ?

have anyone used David to do function enrichment analysis on line ?
i have got one line like bellow:

Category Term Count % PValue Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR

GOTERM_MF_ALL GO:0015924~mannosyl-oligosaccharide mannosidase activity 3 2.70% 0.0026231466883225325 ENSG00000177239, ENSG00000177239, ENSG00000177239, 89 9 10048 37.63295880149813 0.998814050394877 0.9655623809603076 4.540783108986657

that is in this GO:0015924 term, there're 3 genes, but identical, is this bug?
thanks
zslee is offline   Reply With Quote
Old 02-09-2010, 11:14 AM   #2
steven
Senior Member
 
Location: Southern France

Join Date: Aug 2009
Posts: 269
Default

curious indeed.. did you find out where this comes from?
Was the ensembl id triplicated in the original list of gene?
steven is offline   Reply With Quote
Old 02-09-2010, 04:58 PM   #3
zslee
Member
 
Location: shanghai of china

Join Date: May 2009
Posts: 29
Default

i 've checked that, this gene id exist only once in both my test gene list and background
i don't know the resason yet ...
zslee is offline   Reply With Quote
Old 02-15-2010, 09:57 AM   #4
steven
Senior Member
 
Location: Southern France

Join Date: Aug 2009
Posts: 269
Default

if you find out the reason, could you please let us know? thanks a lot!
steven is offline   Reply With Quote
Old 02-15-2010, 06:09 PM   #5
zslee
Member
 
Location: shanghai of china

Join Date: May 2009
Posts: 29
Default

the reason is 3 different David gene id (that they used when do enrichment analysis) mapped to 1 ensemble gene id, the following is the answer from the David Guys:

Ensembl gene id was integrated as a secondary source in the production version of DAVID. Therefore, the coverage is not the best and there are cases where there may be mappings for one Ensembl id to multiple DAVID ids. The latter is the problem with your examples. In the case of ENSG00000198744, it was mapped to 3 DAVID ids which is what is reflected in the chart report. We have recently finished a complete database update that now incorporates Ensembl gene id as a primary source which ensures a mapping of one ensembl id to one DAVID id and with full coverage of Ensembl. The new data is available through our Beta site( http://david.abcc.ncifcrf.gov:8080 ). Please give it a try and let us know what you think.
zslee is offline   Reply With Quote
Old 02-16-2010, 03:52 AM   #6
steven
Senior Member
 
Location: Southern France

Join Date: Aug 2009
Posts: 269
Default

OK I see.. thanks for sharing!
steven 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 10:40 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO