How to get all Pathway annotations for the Agilent Probes (human, mouse, rat)? In Bioconductor there were are some packages availabe like mgug4122a.db, hgug4112a.db and rgug4131a, but they only refer to the 4x44k arrays. I could not find newer versions supporting the 8x60k arrays. Using an online database like BioDBnet (http://biodbnet.abcc.ncifcrf.gov/db/db2db.php) works in principle, but not for ten thousands of genes...
Btw, Agilent says one should download the KEGG database via ftp from KEGG and inport it into GeneSpring. But the referenced ftp server is down and a new server requires a registration. I also don't have GeneSpring.
The BioConductor databases in R for the older array sets were made before KEGG became a for-fee subscription service. Nobody can make such annotation databases for open source software distribution these days, as it would constitute illegal distribution of proprietary intellectual property. Same reason no one can make annotation databases for BioConductor using MetaCore, Ingenuity or any other proprietary genetic database source. It is also the reason why Agilent's own annotations do not include KEGG information (although Agilent's downloadable annotations do include probe GO annotation, since GO is open source and publicly available).
If you want to do large scale batch searches of KEGG like that, your only option is to subscribe to KEGG so you can download the database for your own use.
Otherwise, you are restricted to the available public web tools and data.
Even if you purchased a license for GeneSpring from Agilent, you would also have to subscribe to KEGG if you wish to use the pathways within GeneSpring.
GeneSpring is a useful program, but any program capable of performing database-type functions would suit your needs. This probably isn't a barrier as much as getting access to an annotated database.
If you can't get access to KEGG through a paid subscriber, the public databases may allow you to chase similar questions. For example, you might try PANTHER, http://www.pantherdb.org/about.jsp
Another option is to use UCSC's table browser. You can cross-reference a gene list, such as UCSC genes or Refseq genes, to the KEGG pathway ID. If you can separately map your Agilent probes to these reference mRNAs, you can marry the two datasets. If knowing the KEGG pathway ID# is enough, this is an easy work-around.
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