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.
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.
Authors: Glynn Dennis; Brad T Sherman; Douglas A Hosack; Jun Yang; Wei Gao; H Clifford Lane; Richard A Lempicki Journal: Genome Biol Date: 2003-04-03 Impact factor: 13.583
Authors: M A Harris; J Clark; A Ireland; J Lomax; M Ashburner; R Foulger; K Eilbeck; S Lewis; B Marshall; C Mungall; J Richter; G M Rubin; J A Blake; C Bult; M Dolan; H Drabkin; J T Eppig; D P Hill; L Ni; M Ringwald; R Balakrishnan; J M Cherry; K R Christie; M C Costanzo; S S Dwight; S Engel; D G Fisk; J E Hirschman; E L Hong; R S Nash; A Sethuraman; C L Theesfeld; D Botstein; K Dolinski; B Feierbach; T Berardini; S Mundodi; S Y Rhee; R Apweiler; D Barrell; E Camon; E Dimmer; V Lee; R Chisholm; P Gaudet; W Kibbe; R Kishore; E M Schwarz; P Sternberg; M Gwinn; L Hannick; J Wortman; M Berriman; V Wood; N de la Cruz; P Tonellato; P Jaiswal; T Seigfried; R White Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971
Authors: Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov Journal: Proc Natl Acad Sci U S A Date: 2005-09-30 Impact factor: 11.205
Authors: Douglas A Hosack; Glynn Dennis; Brad T Sherman; H Clifford Lane; Richard A Lempicki Journal: Genome Biol Date: 2003-09-11 Impact factor: 13.583
Authors: Barry R Zeeberg; Haiying Qin; Sudarshan Narasimhan; Margot Sunshine; Hong Cao; David W Kane; Mark Reimers; Robert M Stephens; David Bryant; Stanley K Burt; Eldad Elnekave; Danielle M Hari; Thomas A Wynn; Charlotte Cunningham-Rundles; Donn M Stewart; David Nelson; John N Weinstein Journal: BMC Bioinformatics Date: 2005-07-05 Impact factor: 3.169
Authors: Manhong Dai; Pinglang Wang; Andrew D Boyd; Georgi Kostov; Brian Athey; Edward G Jones; William E Bunney; Richard M Myers; Terry P Speed; Huda Akil; Stanley J Watson; Fan Meng Journal: Nucleic Acids Res Date: 2005-11-10 Impact factor: 16.971
Authors: Brian D Athey; James D Cavalcoli; H V Jagadish; Gilbert S Omenn; Barbara Mirel; Matthias Kretzler; Charles Burant; Raphael D Isokpehi; Charles DeLisi Journal: J Am Med Inform Assoc Date: 2011-11-19 Impact factor: 4.497
Authors: Maureen A Sartor; Alex Ade; Zach Wright; David States; Gilbert S Omenn; Brian Athey; Alla Karnovsky Journal: Bioinformatics Date: 2012-04-06 Impact factor: 6.937
Authors: Nataly Kravchenko-Balasha; Alexander Levitzki; Andrew Goldstein; Varda Rotter; A Gross; F Remacle; R D Levine Journal: Proc Natl Acad Sci U S A Date: 2012-03-05 Impact factor: 11.205
Authors: Steven K Huang; Anne M Scruggs; Jake Donaghy; Richard C McEachin; Aaron S Fisher; Bruce C Richardson; Marc Peters-Golden Journal: FASEB J Date: 2012-05-29 Impact factor: 5.191
Authors: Raymond G Cavalcante; Snehal Patil; Terry E Weymouth; Kestutis G Bendinskas; Alla Karnovsky; Maureen A Sartor Journal: Bioinformatics Date: 2016-01-21 Impact factor: 6.937
Authors: Mark S Doderer; Zachry Anguiano; Uthra Suresh; Ravi Dashnamoorthy; Alexander J R Bishop; Yidong Chen Journal: BMC Genomics Date: 2012-10-26 Impact factor: 3.969
Authors: Richard C McEachin; Nancy L Saccone; Scott F Saccone; Yelena D Kleyman-Smith; Tiara Kar; Rajesh K Kare; Alex S Ade; Maureen A Sartor; James D Cavalcoli; Melvin G McInnis Journal: BMC Med Genet Date: 2010-01-26 Impact factor: 2.103