Literature DB >> 21132056

GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis.

Sachin Mathur1, Mahesh Visvanathan, Stan Svojanovsky, Byunggil Yoo, Adagarla B Srinivas, Gerald H Lushington, Peter G Smith.   

Abstract

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.

Entities:  

Year:  2009        PMID: 21132056      PMCID: PMC2995274          DOI: 10.2174/1875036200903010026

Source DB:  PubMed          Journal:  Open Bioinforma J


  22 in total

1.  KEGG: kyoto encyclopedia of genes and genomes.

Authors:  M Kanehisa; S Goto
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  SCOP: a structural classification of proteins database.

Authors:  L Lo Conte; B Ailey; T J Hubbard; S E Brenner; A G Murzin; C Chothia
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

3.  Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules.

Authors:  J L Sussman; D Lin; J Jiang; N O Manning; J Prilusky; O Ritter; E E Abola
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1998-11-01

4.  DRAGON View: information visualization for annotated microarray data.

Authors:  Christopher M L S Bouton; Jonathan Pevsner
Journal:  Bioinformatics       Date:  2002-02       Impact factor: 6.937

5.  The Gene Ontology (GO) database and informatics resource.

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

6.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.

Authors:  B M Bolstad; R A Irizarry; M Astrand; T P Speed
Journal:  Bioinformatics       Date:  2003-01-22       Impact factor: 6.937

7.  BIND: the Biomolecular Interaction Network Database.

Authors:  Gary D Bader; Doron Betel; Christopher W V Hogue
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

8.  An integrated tool for microarray data clustering and cluster validity assessment.

Authors:  Nadia Bolshakova; Francisco Azuaje; Pádraig Cunningham
Journal:  Bioinformatics       Date:  2004-12-17       Impact factor: 6.937

9.  GenBank.

Authors:  Dennis A Benson; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; David L Wheeler
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

10.  MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation.

Authors:  Leandro Hermida; Olivier Schaad; Philippe Demougin; Patrick Descombes; Michael Primig
Journal:  BMC Bioinformatics       Date:  2006-04-05       Impact factor: 3.169

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