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Gene Set Analysis Toolkit V2 |
| http://bioinfo.vanderbilt.edu/webgestalt | |
| Vanderbilt University | |
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START |
Manual |
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Introduction WebGestalt is a "WEB-based GEne SeT AnaLysis Toolkit". It is designed for functional genomic, proteomic and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides an easy way for biologists to make sense out of gene lists. This is a new version of the original WebGestalt. Major changes in the new version are described in the manual. The GOTM has also been incorporated into this new version of WebGestalt. Please follow the workflow below to analyze your gene lists: 1. Select the organism of interest. 2. Upload a gene/protein list in the txt format, one ID per row. Optionally, a value can be provided for each ID. In this case, put the ID and value in the same row and separate them by a tab. Then pick the ID type that corresponds to the list of IDs. 3. Categorize the uploaded ID list based upon GO Slim. 4. Analyze the uploaded ID list for for enrichment in various biological contexts. You will need to select an appropriate predefined reference set or upload a reference set. If a customized reference set is uploaded, ID type also needs to be selected. After this, select the analysis parameters (e.g., significance level, multiple test adjustment method, etc.). 5. Retrieve enrichment results by opening the respective results files. You may also open and/or download a TSV file, or download the zipped results to a directory on your desktop. Data source The current version of WebGestalt was updated on 1/21/10. It supports eight organisms including human, mouse, rat, worm, fly, yeast, dog, and zebrafish. Information in this version was collected from NCBI Gene (12/16/2009), NCBI GEO (12/16/2009), Ensembl (version 56, 09/23/2009), Gene Ontology (version 1.1.974, 01/21/2010), KEGG (01/21/2010), IPI (01/21/2010), Pathway Commons (01/21/2010), Wikipathways (01/21/2010), MGI (01/21/2010), SGD (01/21/2010), MSigDB (01/21/2010), and through local Computation Analysis (01/21/2010), Affymetrix (12/06/2010), Illumina (12/06/2010), NCBI dbSNP (12/06/2010). Citations 1. Zhang, B., Kirov, S.A., Snoddy, J.R. (2005). WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res, 33(Web Server issue), W741-748. 2. Duncan, D.T., Prodduturi, N., Zhang, B. (2010). WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit. BMC Bioinformatics, 11(Suppl 4):P10. Usage statistics since April 14, 2010 The local usage count is 6122 and the last date of local usage: 05/15/12 The remote usage count is 115885 and the last date of remote usage: 05/16/12 |
RECENT NEWS 12/06/2010 WebGestalt now supports human GWAS studies. IDs from Affymetrix and Illumina Human SNP Arrays are now supported by WebGestalt. Gene lists from Affymetrix SNP 6.0, SNP 5.0, 500K, 100K, and 10K SNP arrays are recognized by both probe IDs and dbSNP rs numbers. Gene lists from Illumina OmniExpres and Omni1_Quad arrays are recognized by dbSNP rs numbers. dbSNP rs numbers that are not on these arrays can also be used as input. In this case, you may choose the genome as a reference for the enrichment analysis. More News |
WebGestalt is currently developed and maintained by Dexter Duncan and Bing Zhang at the Zhang Lab. The project was initiated by Bing Zhang, Stefan Kirov, Denise Schmoyer, and Jay Snoddy in 2003.
Funding credits: NIAAA Integrative Neuroscience Initiative on Alcoholism (U01AA016662, U01AA013512); NIH/NIDA BISTI (P01DA015027); NIH/NIMH (P50MH078028).