Saturday, November 13, 2004

Genomatix 3.2 - Chicken and Rice Genomes

This week Genomatix released version 3.2 of their excellent promoter-analysis software, GenomatixSuite. This follow their last month release of the new and improved GEMS Launcher 4.0. According to the press release, new features / improvements include...

ElDorado / Gene2Promoter
* New genomes:
o Gallus gallus (NCBI build 1 v1)
o Oryza sativa (TIGR release 2)
* Genome updates:
o Human Genome updated to NCBI build 35.
o Mouse Genome updated to NCBI build 33.
* Display of alternative transcripts of a gene in the ElDorado result.
* MatInspector: Export of statistics and common TFs to Excel format.

So now you can do promoter / regulation analysis on the Chicken and Rice Genomes (I'm sure you were all waiting for this, badly, no?). Recent builds of more important genomes (Mouse & Human) fix some errors of previous builds (misallocated contigs, etc).

More importantly, spliced transcripts are viewable from ElDoraro (their Genome Annotation portal), which is very important when doing microarray analysis. Most microarrays don't differentiate between alternative transcripts, and the gene ID often refer to only one of them, so it's good to know that they exist. Most of the time, spliced forms have different functions than the major protein (they can even be implicated in competition / inhibition of the pathway they're part of : no functional domain but can still bind its partners, for example).

I even encountered a case of an upregulated gene, but the most documented protein was (for a long time) the spliced form, which inhibit protein X functions. The full-length protein was discovered only recently, and it turns out that it stimulates protein X. Go figure. No wonder it was the only thing going against all my previous analyses conclusions... now everything is fine. Keep an eye out for these special cases... I think they'll get more frequent as I'm sure we underestimate the role of splicing in a cell.

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