Computational biology and genomics
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…
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…
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
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 process 2 branched chain family amino acid metabolic process 3 regulation of nucleobase, nucleoside, nucleotide…
Updated: 2019 March 24th The Gene Ontology Enrichment Analysis is a popular type of analysis that is carried out after a differential gene expression analysis has been carried out. There are many tools available for performing a gene ontology enrichment analysis. Online tools include DAVID, PANTHER and GOrilla. Bioconductor pacakges include GOstats, topGO and goseq….