search tools and reactome gene sets

[florent dumont]

Hello everybody,

When i used the search tools to select genesets i was wondering if reactome genesets were under-represented in the results ? And when you see page for reactome genesets full description section is empty so it could be linked ?

Thank you very much.

Florent

[Anthony Castanza]

Hi Florent,

There isn't any reason why Reactome gene sets would be under-represented in the search results. Could you perhaps clarify what you mean though? It's a pretty straightforward search tool across the database of sets.

With regard to the full description though, correct, Reactome sets do not populate this information as it is not in the files Reactome provides for our set construction. In order to access these details you would need to follow the link-out to the source data on the Reactome website.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

[florent dumont]

Hi Antony,

Thank you very much for your response. 

Here is an exemple with "apoptosis" keyword that provides this distribution accross c2 and c5 collection:

biocarta celltype      cgn      cgp     gobp     gocc     gomf      hpo   immuno     kegg     onco      pid reactome     wiki
      37        3        1      321       20        1        5        1      106        3       15        1        7        8 

hallmark      chr      cgp biocarta     kegg      pid reactome     wiki      mir      tft      cgn       cm     gobp     gocc
    "50"    "302"   "3494"    "292"    "844"    "196"   "1736"    "830"   "2377"   "1115"    "427"    "431"   "7608"   "1026"
    gomf      hpo     onco   immuno      vax celltype
  "1820"   "5653"    "189"   "4872"    "347"    "840"

We observe 7 genesets for reactome collection which contains 1736 genesets.

So perhaps with more description from reactome it could give more genesets linked to apoptosis ?

Thanks.

Florent