Question

GAGE/Pathview now support 3000 KEGG species and 19 GO species (with BioC 2.14)

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Luo Weijun ★ 1.6k

@luo-weijun-1783

Last seen 17 months ago

United States

Both gage and pathview packages were updated with recently Bioconductor 2.14 release. GAGE/Pathview now support ~ 3000 KEGG species. Function kegg.gsets in gage package is used to generate updated KEGG pathway gene set data. We also added function go.gsets in gage package, which generates up- to-date GO gene sets for 19 common species annotated in Bioconductor and more others by the users. Please check the latest release version for these updates: http://bioconductor.org/packages/release/bioc/html/gage.html http://bioconductor.org/packages/release/bioc/html/pathview.html

GO gage pathview GO gage pathview • 1.6k views

ADD COMMENT • link updated 9.4 years ago by jackipchiho ▴ 10 • written 10.5 years ago by Luo Weijun ★ 1.6k

score 0 · Answer 1 · 2015-06-27

Dear Weijun,

I would like to ask do GAGE applicable to non model species?

My target species are green mussel and intertidal whelk, and I would like to do the gene set enrichment analysis for control (n=3) and chemical treatment groups (n=2 / n=3).

Besides, I have worked out the KEGG (Ko and K number without specific species) and GO (GO number without specific species). Is that possible to customize my own gene annotation file and perform available analysis in GAGE?

Many thanks,

Jack