Literature DB >> 15333457

OntologyTraverser: an R package for GO analysis.

A Young1, N Whitehouse, J Cho, C Shaw.   

Abstract

UNLABELLED: Gene Ontology (GO) annotations have become a major tool for analysis of genome-scale experiments. We have created OntologyTraverser--an R package for GO analysis of gene lists. Our system is a major advance over previous work because (1) the system can be installed as an R package, (2) the system uses Java to instantiate the GO structure and the SJava system to integrate R and Java and (3) the system is also deployed as a publicly available web tool. AVAILABILITY: Our software is academically available through http://franklin.imgen.bcm.tmc.edu/OntologyTraverser/. Both the R package and the web tool are accessible. CONTACT: cashaw@bcm.tmc.edu

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Year:  2004        PMID： 15333457     DOI： 10.1093/bioinformatics/bth495

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


  15 in total

1.  Early patterns of gene expression correlate with the humoral immune response to influenza vaccination in humans.

Authors:  Kristine L Bucasas; Luis M Franco; Chad A Shaw; Molly S Bray; Janet M Wells; Diane Niño; Nancy Arden; John M Quarles; Robert B Couch; John W Belmont
Journal:  J Infect Dis       Date:  2011-02-28       Impact factor: 5.226

2.  Functional annotation of hierarchical modularity.

Authors:  Kanchana Padmanabhan; Kuangyu Wang; Nagiza F Samatova
Journal:  PLoS One       Date:  2012-04-04       Impact factor: 3.240

3.  Recent additions and improvements to the Onto-Tools.

Authors:  Purvesh Khatri; Sivakumar Sellamuthu; Pooja Malhotra; Kashyap Amin; Arina Done; Sorin Draghici
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

4.  Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways.

Authors:  David M Levine; David R Haynor; John C Castle; Sergey B Stepaniants; Matteo Pellegrini; Mao Mao; Jason M Johnson
Journal:  Genome Biol       Date:  2006-10-17       Impact factor: 13.583

5.  BayGO: Bayesian analysis of ontology term enrichment in microarray data.

Authors:  Ricardo Z N Vêncio; Tie Koide; Suely L Gomes; Carlos A de B Pereira
Journal:  BMC Bioinformatics       Date:  2006-02-23       Impact factor: 3.169

6.  WEGO: a web tool for plotting GO annotations.

Authors:  Jia Ye; Lin Fang; Hongkun Zheng; Yong Zhang; Jie Chen; Zengjin Zhang; Jing Wang; Shengting Li; Ruiqiang Li; Lars Bolund; Jun Wang
Journal:  Nucleic Acids Res       Date:  2006-07-01       Impact factor: 16.971

7.  Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations.

Authors:  Steven Van Vooren; Bernard Thienpont; Björn Menten; Frank Speleman; Bart De Moor; Joris Vermeesch; Yves Moreau
Journal:  Nucleic Acids Res       Date:  2007-04-01       Impact factor: 16.971

8.  Induction of the HIV-1 Tat co-factor cyclin T1 during monocyte differentiation is required for the regulated expression of a large portion of cellular mRNAs.

Authors:  Wendong Yu; Yan Wang; Chad A Shaw; Xiao-Feng Qin; Andrew P Rice
Journal:  Retrovirology       Date:  2006-06-09       Impact factor: 4.602

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.  FUNC: a package for detecting significant associations between gene sets and ontological annotations.

Authors:  Kay Prüfer; Bjoern Muetzel; Hong-Hai Do; Gunter Weiss; Philipp Khaitovich; Erhard Rahm; Svante Pääbo; Michael Lachmann; Wolfgang Enard
Journal:  BMC Bioinformatics       Date:  2007-02-06       Impact factor: 3.169
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