Literature DB >> 19717575

Next generation software for functional trend analysis.

Gabriel F Berriz1, John E Beaver, Can Cenik, Murat Tasan, Frederick P Roth.   

Abstract

UNLABELLED: FuncAssociate is a web application that discovers properties enriched in lists of genes or proteins that emerge from large-scale experimentation. Here we describe an updated application with a new interface and several new features. For example, enrichment analysis can now be performed within multiple gene- and protein-naming systems. This feature avoids potentially serious translation artifacts to which other enrichment analysis strategies are subject. AVAILABILITY: The FuncAssociate web application is freely available to all users at http://llama.med.harvard.edu/funcassociate.

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Year:  2009        PMID： 19717575      PMCID： PMC2800365          DOI： 10.1093/bioinformatics/btp498

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  12 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  Characterizing gene sets with FuncAssociate.

Authors:  Gabriel F Berriz; Oliver D King; Barbara Bryant; Chris Sander; Frederick P Roth
Journal:  Bioinformatics       Date:  2003-12-12       Impact factor: 6.937

3.  GeneDB: a resource for prokaryotic and eukaryotic organisms.

Authors:  Christiane Hertz-Fowler; Chris S Peacock; Valerie Wood; Martin Aslett; Arnaud Kerhornou; Paul Mooney; Adrian Tivey; Matthew Berriman; Neil Hall; Kim Rutherford; Julian Parkhill; Alasdair C Ivens; Marie-Adele Rajandream; Bart Barrell
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  Sequence resources at the Candida Genome Database.

Authors:  Martha B Arnaud; Maria C Costanzo; Marek S Skrzypek; Prachi Shah; Gail Binkley; Christopher Lane; Stuart R Miyasato; Gavin Sherlock
Journal:  Nucleic Acids Res       Date:  2006-11-07       Impact factor: 16.971

5.  EcoCyc: a comprehensive view of Escherichia coli biology.

Authors:  Ingrid M Keseler; César Bonavides-Martínez; Julio Collado-Vides; Socorro Gama-Castro; Robert P Gunsalus; D Aaron Johnson; Markus Krummenacker; Laura M Nolan; Suzanne Paley; Ian T Paulsen; Martin Peralta-Gil; Alberto Santos-Zavaleta; Alexander Glennon Shearer; Peter D Karp
Journal:  Nucleic Acids Res       Date:  2008-10-30       Impact factor: 16.971

6.  The Rat Genome Database 2009: variation, ontologies and pathways.

Authors:  Melinda R Dwinell; Elizabeth A Worthey; Mary Shimoyama; Burcu Bakir-Gungor; Jeffrey DePons; Stanley Laulederkind; Timothy Lowry; Rajni Nigram; Victoria Petri; Jennifer Smith; Alexander Stoddard; Simon N Twigger; Howard J Jacob
Journal:  Nucleic Acids Res       Date:  2008-11-07       Impact factor: 16.971

7.  Ensembl 2009.

Authors:  T J P Hubbard; B L Aken; S Ayling; B Ballester; K Beal; E Bragin; S Brent; Y Chen; P Clapham; L Clarke; G Coates; S Fairley; S Fitzgerald; J Fernandez-Banet; L Gordon; S Graf; S Haider; M Hammond; R Holland; K Howe; A Jenkinson; N Johnson; A Kahari; D Keefe; S Keenan; R Kinsella; F Kokocinski; E Kulesha; D Lawson; I Longden; K Megy; P Meidl; B Overduin; A Parker; B Pritchard; D Rios; M Schuster; G Slater; D Smedley; W Spooner; G Spudich; S Trevanion; A Vilella; J Vogel; S White; S Wilder; A Zadissa; E Birney; F Cunningham; V Curwen; R Durbin; X M Fernandez-Suarez; J Herrero; A Kasprzyk; G Proctor; J Smith; S Searle; P Flicek
Journal:  Nucleic Acids Res       Date:  2008-11-25       Impact factor: 16.971

8.  Database resources of the National Center for Biotechnology Information.

Authors:  Eric W Sayers; Tanya Barrett; Dennis A Benson; Stephen H Bryant; Kathi Canese; Vyacheslav Chetvernin; Deanna M Church; Michael DiCuccio; Ron Edgar; Scott Federhen; Michael Feolo; Lewis Y Geer; Wolfgang Helmberg; Yuri Kapustin; David Landsman; David J Lipman; Thomas L Madden; Donna R Maglott; Vadim Miller; Ilene Mizrachi; James Ostell; Kim D Pruitt; Gregory D Schuler; Edwin Sequeira; Stephen T Sherry; Martin Shumway; Karl Sirotkin; Alexandre Souvorov; Grigory Starchenko; Tatiana A Tatusova; Lukas Wagner; Eugene Yaschenko; Jian Ye
Journal:  Nucleic Acids Res       Date:  2008-10-21       Impact factor: 16.971

9.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.

Authors:  Da Wei Huang; Brad T Sherman; Richard A Lempicki
Journal:  Nucleic Acids Res       Date:  2008-11-25       Impact factor: 16.971

10.  WormBase 2007.

Authors:  Anthony Rogers; Igor Antoshechkin; Tamberlyn Bieri; Darin Blasiar; Carol Bastiani; Payan Canaran; Juancarlos Chan; Wen J Chen; Paul Davis; Jolene Fernandes; Tristan J Fiedler; Michael Han; Todd W Harris; Ranjana Kishore; Raymond Lee; Sheldon McKay; Hans-Michael Müller; Cecilia Nakamura; Philip Ozersky; Andrei Petcherski; Gary Schindelman; Erich M Schwarz; Will Spooner; Mary Ann Tuli; Kimberly Van Auken; Daniel Wang; Xiaodong Wang; Gary Williams; Karen Yook; Richard Durbin; Lincoln D Stein; John Spieth; Paul W Sternberg
Journal:  Nucleic Acids Res       Date:  2007-11-08       Impact factor: 16.971
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  144 in total

1.  A Chemoproteomic Strategy for Direct and Proteome-Wide Covalent Inhibitor Target-Site Identification.

Authors:  Christopher M Browne; Baishan Jiang; Scott B Ficarro; Zainab M Doctor; Jared L Johnson; Joseph D Card; Sindhu Carmen Sivakumaren; William M Alexander; Tomer M Yaron; Charles J Murphy; Nicholas P Kwiatkowski; Tinghu Zhang; Lewis C Cantley; Nathanael S Gray; Jarrod A Marto
Journal:  J Am Chem Soc       Date:  2018-12-20       Impact factor: 15.419

2.  Conservation of an RNA regulatory map between Drosophila and mammals.

Authors:  Angela N Brooks; Li Yang; Michael O Duff; Kasper D Hansen; Jung W Park; Sandrine Dudoit; Steven E Brenner; Brenton R Graveley
Journal:  Genome Res       Date:  2010-10-04       Impact factor: 9.043

3.  Making sense out of massive data by going beyond differential expression.

Authors:  Patrick R Schmid; Nathan P Palmer; Isaac S Kohane; Bonnie Berger
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-23       Impact factor: 11.205

4.  Graph-based unsupervised feature selection and multiview clustering for microarray data.

Authors:  Tripti Swarnkar; Pabitra Mitra
Journal:  J Biosci       Date:  2015-10       Impact factor: 1.826

5.  Bach2 maintains T cells in a naive state by suppressing effector memory-related genes.

Authors:  Shin-ichi Tsukumo; Midori Unno; Akihiko Muto; Arata Takeuchi; Kohei Kometani; Tomohiro Kurosaki; Kazuhiko Igarashi; Takashi Saito
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-10       Impact factor: 11.205

6.  SLC7A11 Overexpression in Glioblastoma Is Associated with Increased Cancer Stem Cell-Like Properties.

Authors:  Monika D Polewski; Rosyli F Reveron-Thornton; Gregory A Cherryholmes; Georgi K Marinov; Karen S Aboody
Journal:  Stem Cells Dev       Date:  2017-07-27       Impact factor: 3.272

7.  Genome-Wide Analysis of Starvation-Selected Drosophila melanogaster-A Genetic Model of Obesity.

Authors:  Christopher M Hardy; Molly K Burke; Logan J Everett; Mira V Han; Kathryn M Lantz; Allen G Gibbs
Journal:  Mol Biol Evol       Date:  2018-01-01       Impact factor: 16.240

8.  Leukocyte protease binding to nucleic acids promotes nuclear localization and cleavage of nucleic acid binding proteins.

Authors:  Marshall P Thomas; Jennifer Whangbo; Geoffrey McCrossan; Aaron J Deutsch; Kimberly Martinod; Michael Walch; Judy Lieberman
Journal:  J Immunol       Date:  2014-04-25       Impact factor: 5.422

9.  Computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks.

Authors:  Sudipto Saha; Jean-Eudes Dazard; Hua Xu; Rob M Ewing
Journal:  J Proteome Res       Date:  2012-08-21       Impact factor: 4.466

10.  Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling.

Authors:  Jun Inoue; Yukuto Sato; Robert Sinclair; Katsumi Tsukamoto; Mutsumi Nishida
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-17       Impact factor: 11.205
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