1. ConceptGen: a gene set enrichment and gene set relation mapping tool
- Author
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Alla Karnovsky, James D. Cavalcoli, H. V. Jagadish, Maureen A. Sartor, Vasudeva Mahavisno, Gilbert S. Omenn, Venkateshwar G. Keshamouni, Barbara Mirel, Zach Wright, Brian D. Athey, Terry E. Weymouth, and Rork Kuick
- Subjects
Male ,Statistics and Probability ,Relation (database) ,Gene regulatory network ,Computational biology ,Biology ,computer.software_genre ,Biochemistry ,Health informatics ,Pattern Recognition, Automated ,Data modeling ,Set (abstract data type) ,Gene mapping ,Transforming Growth Factor beta ,Databases, Genetic ,Animals ,Humans ,Gene Regulatory Networks ,Neoplasm Metastasis ,Molecular Biology ,Oligonucleotide Array Sequence Analysis ,business.industry ,Gene Expression Profiling ,Computational Biology ,Original Papers ,Computer Science Applications ,Pancreatic Neoplasms ,Gene expression profiling ,Computational Mathematics ,Computational Theory and Mathematics ,Pattern recognition (psychology) ,Data mining ,business ,computer ,Software - Abstract
Motivation: The elucidation of biological concepts enriched with differentially expressed genes has become an integral part of the analysis and interpretation of genomic data. Of additional importance is the ability to explore networks of relationships among previously defined biological concepts from diverse information sources, and to explore results visually from multiple perspectives. Accomplishing these tasks requires a unified framework for agglomeration of data from various genomic resources, novel visualizations, and user functionality. Results: We have developed ConceptGen, a web-based gene set enrichment and gene set relation mapping tool that is streamlined and simple to use. ConceptGen offers over 20 000 concepts comprising 14 different types of biological knowledge, including data not currently available in any other gene set enrichment or gene set relation mapping tool. We demonstrate the functionalities of ConceptGen using gene expression data modeling TGF-beta-induced epithelial-mesenchymal transition and metabolomics data comparing metastatic versus localized prostate cancers. Availability: ConceptGen is part of the NIH's National Center for Integrative Biomedical Informatics (NCIBI) and is freely available at http://conceptgen.ncibi.org. For terms of use, visit http://portal.ncibi.org/gateway/pdf/Terms%20of%20use-web.pdf Contact: conceptgen@umich.edu; sartorma@umich.edu Supplementary information: Supplementary data are available at Bioinformatics online.
- Published
- 2009