GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis

Sachin, Mathur; Mahesh, Visvanathan; Stan, Svojanovsky; Byunggil, Yoo; Adagarla B., Srinivas; Gerald H., Lushington; Peter G., Smith

GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis

Mathur Sachin^{#, 1}, Visvanathan Mahesh^{*, #, 2, 3}, Svojanovsky Stan^{2, 4, 5}, Yoo Byunggil^{2, 4, 5}, Srinivas Adagarla B.³, Lushington Gerald H.³, Smith Peter G.^{2, 4, 5}

¹ School of Computing and Engineering, University of Missouri-Kansas City, MO 64110, USA

² Department of Integrative and Molecular Physiology, University of Kansas Medical Center, Kansas City, Kansas 66160 USA

³ Bioinformatics Core Facility, University of Kansas, Lawrence, KS 66047,USA

⁴ Bioinformatics Core, Kansas IDeA Network for Biomedical Research Excellence (K-INBRE), Mailstop 3051, University of Kansas Medical Center, Kansas City, Kansas 66160 USA

⁵ RL Smith Mental Retardation Research Center, University of Kansas Medical Center, Kansas City, Kansas 66160 USA

Article Information

Identifiers and Pagination:

Year: 2009
Volume: 3
First Page: 26
Last Page: 30
Publisher ID: TOBIOIJ-3-26
DOI: 10.2174/1875036200903010026

Article History:

Received Date: 17/02/2009
Revision Received Date: 24/04/2009
Acceptance Date: 24/04/2009
Electronic publication date: 16/07/2009
Collection year: 2009

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© 2009 Sachin et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: https://creativecommons.org/licenses/by/4.0/legalcode. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

^* Address correspondence to this author at the Department of Integrative and Molecular Physiology, University of Kansas Medical Center, Kansas City, Kansas 66160 USA; E-mail: mvisvanathan@ku.edu
^# Authors have equally contributed.

We have developed the web based tool GOAPhAR (Gene Ontology, Annotations and Pathways for Array Research), that integrates information from disparate sources regarding gene annotations, protein annotations, identifiers associated with probe sets, functional pathways, protein interactions, Gene Ontology, publicly available microarray datasets and tools for statistically validating clusters in microarray data. Genes of interest can be input as Affymetrix probe identifiers, Genbank, or Unigene identifiers for human, mouse or rat genomes. Results are provided in a user friendly interface with hyperlinks to the sources of information.

The tool is freely available at http://bioinformatics.kumc.edu/goaphar/.

Keywords: GOAPhAR, Gene ontology, Annotations and pathways for array research.

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RESEARCH ARTICLE

GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis

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