goseq using pnas_expression_filtered.tsv

goseq is a Bioconductor package for performing a gene ontology analysis for RNA-seq and other length biased data. For more information on how to use the package, please refer to the vignette. For more information on the pnas_expression file please refer to my older post. The x-axis of the plot above are binned lengths of...

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Bidirectional genes

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 as the universe list: Although this was a brief analysis, the results are somewhat similar...

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Gene Ontology enrichment analysis

Updated: 2013 November 23rd There are many tools available for conducting a gene ontology enrichment analysis. Some online tools that I've heard of are DAVID, PANTHER and GOrilla but I have never actually used them. Within Bioconductor there's GOstats, topGO and goseq (and probably some more). Here I'll test out GOstats and topGO. Firstly download...

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