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Canonical Pathway Analysis Using Gene Expression with GOPHER Web Tool

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Hundreds of canonical biological networks have been discovered and annotated, and are freely accessible through online resources such as Kegg, Biocarta, Genmapp, and the Gene Ontology Consortium. Using statistical tests, it is possible to prioritize biological networks from these resources that are most relevant to a given set of target genes. The statistical ranking of these networks is further enhanced by the inclusion of microarray gene expression data. We designed the web tool GOPHER (Gene Ontology and Pathway Hierarchy EncodeR) for this purpose. In GOPHER, users can select up to three statistical tests to perform on a set of target genes, namely Fisher's Exact Test, Mahalanobis Distance Test, and Hotelling's T-Square Test, the latter two being multivariate tests which factor in expression data differences across biological states. Users can also select which resources they wish to draw from, including Gene Ontology and the Kegg, Biocarta, and Genmapp pathway databases. Upon completion of the selected statistical tests, relevant pathways and/or ontologies are displayed in a table, each pathway/ontology being expandable to show the genes contained within it, with hypertext links to Kegg, Biocarta, GenBank, etc for each pathway/gene. The table is also sortable according to each of the three aforementioned statistical ranks and output is further enhanced through the use of bar charts showing the different test results in graphical format. The results are also able to be exported for later use by the researcher. This web tool stands out among freely available pathway/ontology web tools in that it allows for the use of gene expression and multivariate statistics in the ranking of results, while others do not.

Last updated November 16, 2007