Tag Archives: GO

Bidirectional genes

Posted on September 14, 2011 by Davo

Download 5′ UTR for all RefSeq genes using the UCSC Table Browser. Separate features according to strand Use intersectBed to find overlapping features Performing a GO enrichment analysis on the unique list of bidirectional genes and using all the genes … Continue reading →

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Extract gene names according to GO terms

Posted on May 20, 2011 by Davo

Find genes that are associated with a known gene ontology term: See also: org.Hs.eg.db Source: bioconductor mailing list thread -> [BioC] Query Gene Ontology

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Of the RefSeq’s that have CpG islands 1,000 bp upstream, what are the GO terms – part 2?

Posted on November 16, 2010 by Davo

Using GO.db and GOstats, I obtained the gene list with bona fide CpG islands upstream and conducted a GO enrichment analysis. The choice of the gene universe is again all RefSeq gene models. Enriched Biological Processes include: 1 primary metabolic … Continue reading →

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Gene Ontology enrichment analysis

Posted on November 10, 2010 by Davo

Using R, we need these packages: “GO.db” and “GOstats”. Instructions for installing these packages are here. I work with RefSeq’s; the GOstats package requires Entrez ID’s. Use refseq2entrez.pl to convert the IDs. For this analysis, my universe list is every … Continue reading →

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