GO-Elite in Bioinformatics and Expanded Features

[Nathan Salomonis]

We are pleased to announce the release of our latest version of GO-Elite, now described in the journal of Bioinformatics. GO-Elite version 1.25 provides a leap forward in the analysis of both gene and metabolomics data for a vast array of species. In addition to supporting over over 60 species and 50 ID systems, the latest version includes databases for gene, disease and phenotype ontologies, multiple pathway databases, domains, biomarkers, and transcription factor and microRNA targets.  Pathway visualization is facilitated directly within the stand-alone software as well as within GenMAPP-CS following over-representation.  Also included are improved options for species or ID system addition, inclusion of new ontologies or pathways and relationship customization.

 

GO-Elite is available as a web interface, extensions to the programs GenMAPP-CS and AltAnalyze and as a cross-platform application.

The Bioinformatics Application Note can be viewed at:

http://code.google.com/p/go-elite/wiki/AboutUs#Citing_GO-Elite

Best Regards,

Nathan

[Sheena Lee]

Hello,

 

Are exon array core probe sequences supported by GO-Elite?

 

Best Wishes

 

Sheena

[Nathan Salomonis]

Hi Sheena,

Yes, all probesets (exon-level) and transcript cluster identifiers are supported. These are those that are annotated according to Ensembl as belonging to that gene ID. Relationships are stored in the file Databases/EnsMart62Plus/uid-gene/Ensembl-Affymetrix.txt.

As an aside, if you analyze your exon array data files in GO-Elite's sister program AltAnalyze (http://altanalyze.org), it will automate your analysis all levels (CEL->Expression->Statistics->Clusters->AltSplice->GO-Elite). The results from AltAnalyze will be provided using AltAnalyze's annotation pipeline for assigning core, extended and full probesets based on mRNA evidence from that build of Ensembl/UCSC. I highly recommend this.

Best,
Nathan

--
You received this message because you are subscribed to the Google Groups "GO-Elite" group.
To post to this group, send email to go-e...@googlegroups.com.
To unsubscribe from this group, send email to go-elite+u...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/go-elite?hl=en.

[Sheena Lee]

Hello Nathan,

 

I’ve tried putting the attached Affymetrix exon array expression data into GO-Elite and get the error message described in the attached report file.  Not sure what’s going on.  I’m using the latest version of GO-Elite and EnsMart62Plus.

 

Best Wishes

 

Sheena

[Nathan Salomonis]

Hi Sheena,

Either Ensembl used to have the transcript-level annotations for the Exon arrays or I was wrong that they were in the Ensembl data we get. The exon-level probesets are there but not the transcript-level. Also, we supplement the annotations with those directly from Affy, but it looks like we hadn't been including the transcript-level exon annotations in our build either (will do for the next build).

However, that's the cool thing about GO-Elite, you can just easily add them!

The relationship file is attached containing these relationships. To quickly add to your version, simply open the program directory and find: Databases/EnsMart62Plus/Mm/uid-gene and replace the existing with the attached. This can also be done in the program using the directions for "Add New Relationship Files" here:

http://www.genmapp.org/go_elite/help.htm#new_species

To get this file, I simply downloaded the most recent Affymetrix transcript annotation file from here:

http://www.affymetrix.com/analysis/downloads/na32/wtexon/MoEx-1_0-st-v1.na32.mm9.transcript.csv.zip

Then I followed these instructions in GO-Elite:

http://genmapp.org/go_elite/help.htm

See sections:

Modifying Species Databases 

and

Updating Affymetrix Relationships

Let me know if you have any other questions.

Best,

Nathan