Question: (Gene-set)Pathway analysis based on network/pathway topology in R
gravatar for svlachavas
4.4 years ago by
Greece/Athens/National Hellenic Research Foundation
svlachavas740 wrote:

Dear Bioconductor Community,

based on my current project, except from very efficient functional enrichment tests like mroast or even simple implementations such as ORA regarding some DEG lists i acquired from limma, i would like also to implement some pathway analysis based on network topology, to strengthen more my results and/or maybe get some interesting modules regarding some possible gene-networks perturbated in my analysis. I have used in the past the R package SPIA, but unfortunately it has stop updating since 2012 regarding the outdated KEGG data. I checked that the newer version of SPIA and although it has a way of "manually" pass up-to-date KEGG xml files, still to download from KEGG site all pathways(or the majority of human pathways to test) it still laborious. So, i would like to ask if there are other known R packages which implement network/pathway topology and have been used for pathway analysis and also have up-to-date annotation data ??

Thank you in advance !!

ADD COMMENTlink written 4.4 years ago by svlachavas740

Hi ,

Please seeĀ SPIA algorithm organisms not included already in the SPIA package for some info on how to use R to download recent KEGG xml files for use with SPIA.

Adi Tarca

ADD REPLYlink written 4.4 years ago by Tarca, Adi570

Dear Mr. Tarca,

thank you for your answer-so just to confirm my procedure from your link above, i just have to include in the function keggGet() the codes(in hsa format) of the pathways i want to include in my analysis ? Furthermore, afterwards how i could implement the specific downloaded-returned pathways via the spia() function ?



ADD REPLYlink written 4.4 years ago by svlachavas740
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