title: ConceptGen: a gene set enrichment and gene set relation mapping tool.
abstract: BACKGROUND
  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.
authors.affiliation: Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA. sartorma@umich.edu
authors.forename: Maureen A
authors.initials: MA
authors.lastname: Sartor
authors.forename: Vasudeva
authors.initials: V
authors.lastname: Mahavisno
authors.forename: Venkateshwar G
authors.initials: VG
authors.lastname: Keshamouni
authors.forename: James
authors.initials: J
authors.lastname: Cavalcoli
authors.forename: Zachary
authors.initials: Z
authors.lastname: Wright
authors.forename: Alla
authors.initials: A
authors.lastname: Karnovsky
authors.forename: Rork
authors.initials: R
authors.lastname: Kuick
authors.forename: H V
authors.initials: HV
authors.lastname: Jagadish
authors.forename: Barbara
authors.initials: B
authors.lastname: Mirel
authors.forename: Terry
authors.initials: T
authors.lastname: Weymouth
authors.forename: Brian
authors.initials: B
authors.lastname: Athey
authors.forename: Gilbert S
authors.initials: GS
authors.lastname: Omenn
mesh_terms: D000818:Animals; D019295:Computational Biology; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D006801:Humans; D008297:Male; D009362:Neoplasm Metastasis / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D010190:Pancreatic Neoplasms / Q000235:genetics; D010363:Pattern Recognition, Automated / Q000379:methods*; D012984:Software; D016212:Transforming Growth Factor beta / Q000235:genetics / Q000378:metabolism
chemical_list: D016212:Transforming Growth Factor beta