• ArrayQuest: a web resource for...

*Result*: ArrayQuest: a web resource for the analysis of DNA microarray data.

Title:
ArrayQuest: a web resource for the analysis of DNA microarray data.
Authors:
Argraves GL; Array Genetics, Inc,, 59 Great Quarter Road, Newtown, CT 06482, USA. argraves@musc.edu, Jani S, Barth JL, Argraves WS
Source:
BMC bioinformatics [BMC Bioinformatics] 2005 Dec 01; Vol. 6, pp. 287. Date of Electronic Publication: 2005 Dec 01.
Publication Type:
Journal Article; Research Support, N.I.H., Extramural
Language:
English
Journal Info:
Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: [London] : BioMed Central, 2000-
MeSH Terms:
Computational Biology/*methods , Gene Expression Profiling/*methods , Oligonucleotide Array Sequence Analysis/*methods, DNA/chemistry ; Algorithms ; Cluster Analysis ; Computer Graphics ; Data Interpretation, Statistical ; Database Management Systems ; Databases, Factual ; Databases, Genetic ; Databases, Nucleic Acid ; Databases, Protein ; Gene Library ; Information Storage and Retrieval ; Internet ; Programming Languages ; Software ; User-Computer Interface
References:
Bioinformatics. 2004 Dec 12;20(18):3656-8. (PMID: 15247094)
Biotechniques. 2003 Mar;Suppl:45-51. (PMID: 12664684)
Genome Res. 2001 Sep;11(9):1603-10. (PMID: 11544205)
Genome Biol. 2004;5(10):R80. (PMID: 15461798)
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W638-43. (PMID: 15980552)
Bioinformatics. 2003 Dec 12;19(18):2473-4. (PMID: 14668234)
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W457-9. (PMID: 15215429)
Nucleic Acids Res. 2003 Jul 1;31(13):3461-7. (PMID: 12824345)
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W441-4. (PMID: 15215426)
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W465-70. (PMID: 15215431)
Grant Information:
P20 RR016434 United States RR NCRR NIH HHS; R24 CA095841 United States CA NCI NIH HHS; P20RR016434 United States RR NCRR NIH HHS; R24CA095841 United States CA NCI NIH HHS
Substance Nomenclature:
9007-49-2 (DNA)
Entry Date(s):
Date Created: 20051203 Date Completed: 20060126 Latest Revision: 20240412
Update Code:
20260130
PubMed Central ID:
PMC1325052
DOI:
10.1186/1471-2105-6-287
PMID:
16321157
Database:
MEDLINE

*Further Information*

*Background: Numerous microarray analysis programs have been created through the efforts of Open Source software development projects. Providing browser-based interfaces that allow these programs to be executed over the Internet enhances the applicability and utility of these analytic software tools.
Results: Here we present ArrayQuest, a web-based DNA microarray analysis process controller. Key features of ArrayQuest are that (1) it is capable of executing numerous analysis programs such as those written in R, BioPerl and C++; (2) new analysis programs can be added to ArrayQuest Methods Library at the request of users or developers; (3) input DNA microarray data can be selected from public databases (i.e., the Medical University of South Carolina (MUSC) DNA Microarray Database or Gene Expression Omnibus (GEO)) or it can be uploaded to the ArrayQuest center-point web server into a password-protected area; and (4) analysis jobs are distributed across computers configured in a backend cluster. To demonstrate the utility of ArrayQuest we have populated the methods library with methods for analysis of Affymetrix DNA microarray data.
Conclusion: ArrayQuest enables browser-based implementation of DNA microarray data analysis programs that can be executed on a Linux-based platform. Importantly, ArrayQuest is a platform that will facilitate the distribution and implementation of new analysis algorithms and is therefore of use to both developers of analysis applications as well as users. ArrayQuest is freely available for use at http://proteogenomics.musc.edu/arrayquest.html.*