[BioC] Bioconductor Digest, Vol 94, Issue 10

[Tarca, Adi]

>From: Bhaskar Dutta <bhaskar.dutta at ...>
>Subject: SPIA package with updated KEGG pathways
>Newsgroups: gmane.science.biology.informatics.conductor
>Date: 2010-12-08 17:22:43 GMT (2 days, 2 hours and 45 minutes ago)

>Hello,

>KEGG pathways were recently updated. How can I use the SPIA package
>with the updated KEGG pathways?

>thanks
>Bhaskar


Hi Bhaskar,

The latest KEGG data matrices for SPIA for most organisms in KEGG are at: http://bioinformaticsprb.med.wayne.edu/SPIA/SPIA_KEGG_dec082010/

Note that not all the pathways get parsed to be used in the pathway analysis. For instance, starting with 135 non-metabolic pathways, 
115 remain after dropping those without any relations (edges),
113 remain after dropping those with only "expression" type of relations (since by default SPIA does not use this type of relation),
112 remain after dropping one pathway that had relations but the relations were between groups/objects that did not contain genes.

Regards,
Adi Tarca