GBIRG ontology study: which pathway analysis package will best suite my data?

摘要

Pathway analysis is a critical step in a large fraction of bioinformatics projects. In these analyses, gene lists or ranked gene lists derived from any number of different methods including RNAseq, microarrays, ChIPseq, etc., are compared to databases of gene annotations and pathways are identified that are enriched for genes in the submitted gene sets. Numerous tools, both commercial and open source, are available to do pathway analysis, differing the statistical approaches used and the lists of annotations available. Identifying the ‘right’ pathway analysis tool for a bioinformatician to use in a specific situation is an art at best, and mostly reflects personal bias of the informatician as broad comparative studies are hard to do. GBIRG conducted a series of ‘case studies,’ comparing different pathway analysis tools across a number of published datasets and looking for themes in the behavior of the tools and summarized the results.