about David, why one gene is calculated 3 times ?

zslee · 02-08-2010, 06:15 AM

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

steven · 02-09-2010, 11:14 AM

curious indeed.. did you find out where this comes from?
Was the ensembl id triplicated in the original list of gene?

zslee · 02-09-2010, 04:58 PM

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 ...

steven · 02-15-2010, 09:57 AM

if you find out the reason, could you please let us know? thanks a lot!

zslee · 02-15-2010, 06:09 PM

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.

steven · 02-16-2010, 03:52 AM

OK I see.. thanks for sharing!

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02-08-2010, 06:15 AM	#1
zslee Member Location: shanghai of china Join Date: May 2009 Posts: 29	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

02-09-2010, 11:14 AM	#2
steven Senior Member Location: Southern France Join Date: Aug 2009 Posts: 269	curious indeed.. did you find out where this comes from? Was the ensembl id triplicated in the original list of gene?

02-09-2010, 04:58 PM	#3
zslee Member Location: shanghai of china Join Date: May 2009 Posts: 29	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 ...

02-15-2010, 09:57 AM	#4
steven Senior Member Location: Southern France Join Date: Aug 2009 Posts: 269	if you find out the reason, could you please let us know? thanks a lot!

02-15-2010, 06:09 PM	#5
zslee Member Location: shanghai of china Join Date: May 2009 Posts: 29	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.

02-16-2010, 03:52 AM	#6
steven Senior Member Location: Southern France Join Date: Aug 2009 Posts: 269	OK I see.. thanks for sharing!