5.4 years ago by
Bergen, Norway
Most tools I have found do not work with custom annotations or other organisms than predefined (which is a shame imo). Certainly, nobody would ever want to do research on other organisms than mouse, human, or drosophila.
Edit: What is more, most tools do not allow you restrict the background set of genes, such that they will always use the complete genome, something which makes them rather undesirable in many cases (not possibly to restrict to relevant genes only, e.g. those represented by microarray probes, or expressed at least once in a study).
So there are two features you should look for in a GO-enrichment tool for non-model organisms:
- ability to define own GO annotation and
- ability to define own background gene set
The Bioconductor package GOstats however will work with non-model organisms, you only need an annotation data.frame with three columns: go_id, evidence code, gene-id. that should be easy to generate from the Blast2GO output, see:
http://www.bioconductor.org/packages/release/bioc/vignettes/GOstats/inst/doc/GOstatsForUnsupportedOrganisms.pdf
evidence code should possibly be set to be 'IEA' for automatic annotation pipelines like Blast2GO or InterPro.
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modified 5.4 years ago
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5.4 years ago by
Dr. Mabuse ♦ 47k
I did GO enrichment by downloading GO cc, mf and bp lists, searching my GO's in the list using dictionary and counting a frequency of occurrence of each GO term and produce an enrichment histogram.