Annotation issue?

[Sheena Lee]

Hello,

 

1) I’ve put some Affymetrix Exon microarray data into GO-Elite using the Entrez ID as the identifier.

 

2) I’ve then had a look at the MAPPFinder results and can see that 3 of 5 genes in the GO term Cell Proliferation in Dorsal Spinal Cord are altered.

 

 

GOID	GO Name	GO Type	Number Changed	Number Measured	Number in GO	Percent Changed	Percent Present	Z Score	PermuteP	AdjustedP
10456	cell proliferation in dorsal spinal cord	P	3	5	5	60	100	6.017698	0.002	0.138

 

 

 

3) If I then look at the Entrez gene associations file I can see that the following genes are changed in that GO term.

 

107751	Prrxl1	paired related homeobox protein-like 1	107751	10456	cell proliferation in dorsal spinal cord	-1.5	410	269
15416	Hoxb8	homeo box B8	15416	10456	cell proliferation in dorsal spinal cord	-1.5	696	459
18516	Pbx3	pre B-cell leukemia transcription factor 3	18516	10456	cell proliferation in dorsal spinal cord	-1.5	1021	663

 

 

4) If I then go to AMIGO and search for genes involved with Cell Proliferation in Dorsal Spinal Cord there are 2 genes associated which are very different from the 3 above (see screen shot below).  Does anyone know why this is.

 

 

Best Wishes

 

Sheena Lee

 

[Nathan Salomonis]

Hi Sheena,

 

Thank you for using GO-Elite. For some reason, AMIGO doesn't have good gene annotations for all supported species (in the image below only zebrafish genes are shown). The best place to look at the source GO annotations when using EntrezGene is EntrezGene. If you go to their website and look for these genes you will see these GO annotations. I assume you also found the "combined" files in the "GO-Elite_results" folder. These files also inlcude the gene symbols in the same line as the results. This can save some time. Also, we have written an application for doing exon array splicing analyses which may interest you named AltAnalyze (http://www.altanalyze.org), which allows you to load CEL files, run RMA, get a gene expression summary (annotated by Ensembl genes and based on constitutive probesets) and get predicted alternative splicing events with functional predictions (changes in protein domains/miRNA binding sites due to alternative exon regulation).

 

Best,

Nathan