Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W621-6.

ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics.

Chung HJ, Park CH, Han MR, Lee S, Ohn JH, Kim J, Kim J, Kim JH.

Source

Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul 110-799, Korea.

Abstract

Summary: ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics (SVG). Deciphering the crosstalk among pathways and integrating biomedical ontologies and knowledge bases may help biological interpretation of microarray data. ArrayXPath is empowered by integrating gene-pathway, disease-pathway, drug-pathway and pathway-pathway correlations with integrated Gene Ontology, Medical Subject Headings and OMIM Morbid Map-based annotations. We applied Fisher's exact test and relative risk to evaluate the statistical significance of the correlations. ArrayXPath produces Javascript-enabled SVGs for web-enabled interactive visualization of gene-expression profiles integrated with gene-pathway-disease interactions enriched by biomedical ontologies.

PMID:: 15980549; [PubMed - indexed for MEDLINE]
PMCID:: PMC1160211

Free PMC Article

Images from this publication.See all images (2) Free text

Publication Types, MeSH Terms

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

LinkOut - more resources

Full Text Sources

Molecular Biology Databases

ArrayXPath - Bioinformatics.ca Links Directory

Supplemental Content

Save items

Related citations in PubMed

ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics. [Nucleic Acids Res. 2004]
ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics.
Chung HJ, Kim M, Park CH, Kim J, Kim JH. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W460-4.
ChromoViz: multimodal visualization of gene expression data onto chromosomes using scalable vector graphics. [Bioinformatics. 2004]
ChromoViz: multimodal visualization of gene expression data onto chromosomes using scalable vector graphics.
Kim J, Chung HJ, Park CH, Park WY, Kim JH. Bioinformatics. 2004 May 1; 20(7):1191-2. Epub 2004 Feb 5.
BioLattice: a framework for the biological interpretation of microarray gene expression data using concept lattice analysis. [J Biomed Inform. 2008]
BioLattice: a framework for the biological interpretation of microarray gene expression data using concept lattice analysis.
Kim J, Chung HJ, Jung Y, Kim KK, Kim JH. J Biomed Inform. 2008 Apr; 41(2):232-41. Epub 2007 Nov 1.
Review Interpreting microarray results with gene ontology and MeSH. [Methods Mol Biol. 2007]
Review Interpreting microarray results with gene ontology and MeSH.
Osborne JD, Zhu LJ, Lin SM, Kibbe WA. Methods Mol Biol. 2007; 377:223-42.
Review An overview of Spotfire for gene-expression studies. [Curr Protoc Bioinformatics. 2004]
Review An overview of Spotfire for gene-expression studies.
Kaushal D, Naeve CW. Curr Protoc Bioinformatics. 2004 Sep; Chapter 7:Unit 7.7.

See reviews... See all...

Cited by 17 PubMed Central articles

Comprehensive evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data. [BMC Bioinformatics. 2011]
Comprehensive evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data.
Kim MH, Seo HJ, Joung JG, Kim JH. BMC Bioinformatics. 2011 Nov 30; 12 Suppl 13:S8. Epub 2011 Nov 30.
graphite - a Bioconductor package to convert pathway topology to gene network. [BMC Bioinformatics. 2012]
graphite - a Bioconductor package to convert pathway topology to gene network.
Sales G, Calura E, Cavalieri D, Romualdi C. BMC Bioinformatics. 2012 Jan 31; 13:20. Epub 2012 Jan 31.
SEAS: a system for SEED-based pathway enrichment analysis. [PLoS One. 2011]
SEAS: a system for SEED-based pathway enrichment analysis.
Mao X, Zhang Y, Xu Y. PLoS One. 2011; 6(7):e22556. Epub 2011 Jul 22.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

ArrayXPath II: mapping and visualizing microarray gene-expression data with biom...
ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W621-6.

PubMed
E-RNAi: a web application to design optimized RNAi constructs.
E-RNAi: a web application to design optimized RNAi constructs.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W582-8.

PubMed
Dcode.org anthology of comparative genomic tools.
Dcode.org anthology of comparative genomic tools.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W56-64.

PubMed
POWER: PhylOgenetic WEb Repeater--an integrated and user-optimized framework for...
POWER: PhylOgenetic WEb Repeater--an integrated and user-optimized framework for biomolecular phylogenetic analysis.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W553-6.

PubMed
PriFi: using a multiple alignment of related sequences to find primers for ampli...
PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W516-20.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: