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Wikiomics:Pathway analysis: Difference between revisions
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* [http://kobas.cbi.pku.edu.cn. KOBAS] server used for i.e. elucidating pathways in addicion | * [http://kobas.cbi.pku.edu.cn. KOBAS] server used for i.e. elucidating pathways in addicion | ||
Li, Chuan-Yun, Xizeng Mao, and Liping Wei. “Genes and (Common) Pathways Underlying Drug Addiction.” PLoS Computational Biology 4, no. 1 (1, 2008) [http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0040002 HTML] | ** takes both FASTA files and lists of genes | ||
** caveat: excise '''gi|''' from typical FASTA NCBI entry to get unique IDs | |||
** Li, Chuan-Yun, Xizeng Mao, and Liping Wei. “Genes and (Common) Pathways Underlying Drug Addiction.” PLoS Computational Biology 4, no. 1 (1, 2008) [http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0040002 HTML] | |||
* GSEA http://www.broad.mit.edu/gsea/software/software_index.html | * GSEA http://www.broad.mit.edu/gsea/software/software_index.html | ||
objections (Damian D, Gorfine M. Statistical concerns about the GSEA procedure): http://www.nature.com/ng/journal/v36/n7/full/ng0704-663a.html | objections (Damian D, Gorfine M. Statistical concerns about the GSEA procedure): http://www.nature.com/ng/journal/v36/n7/full/ng0704-663a.html | ||
