Mathematical and Statistical Computing Lab




Developed by: Peter J. Munson and Jennifer J. Barb



Introduction - GO-SCAN is a bioinformatics tool that selects and presents relevant Gene Ontology (GO) annotations for a list of differentially expressed genes ("hit" list) from an Affymetrix microarray experiment. A Fisher's exact test is used to select statistically relevant genes and report a p-value for each gene. Probe sets on the Affymetrix chip are first mapped to their corresponding Entrez Gene ID, then to their GO annotations. Annotations used in GO-SCAN are derived from the Affymetrix web site and from the Gene Ontology consortium. In applications, GOSCAN has allowed users to quickly discover themes and pathways related to the experimental perturbation or disease under study. GO-SCAN has been tested on human, rat, mouse and yeast chips and was presented at NIH Research Festival 2004. View poster here.

  • GO-SCAN Online - Web interface easily accessible from any browser and any platform to run GO-SCAN without the need to install any software. Results are displayed as a web page containing an expandable list structure presenting the relevant annotations in an order according to their position within the ontology hierarchy. Optionally, the foldchange or p-value can be used to order the genes within each term.

  • GO-SCAN using JMP - JMP must be installed locally (for more information go to JMP homepage at www.jmp.com. Text output is produced from running a GO-SCAN JMP script. In order to view text output as a collapsible list text file must be formatted and viewed in MS Excel. Click here to see a sample output. Download GO-SCAN JMP script here.

  • GO-Map using JMP - GO-Map is generated from the GO-SCAN JMP script and is a two-way hierarchical cluster heatmap displaying genes ordered into groups sharing similar GO annotations. GO terms are clustered when they annotate a similar list of genes. This visualization is available as a text file from a JMP script that must be formatted and viewed in MS Excel. Click here to see a sample output.

    • Last updated: March 15, 2006

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