ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics
Open Access
- 1 July 2005
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 33 (Web Server) , W621-W626
- https://doi.org/10.1093/nar/gki450
Abstract
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.Keywords
This publication has 13 references indexed in Scilit:
- Ontologizing gene-expression microarray data: characterizing clusters with Gene OntologyBioinformatics, 2004
- Statistical significance for genomewide studiesProceedings of the National Academy of Sciences, 2003
- Module networks: identifying regulatory modules and their condition-specific regulators from gene expression dataNature Genetics, 2003
- GoMiner: a resource for biological interpretation of genomic and proteomic dataGenome Biology, 2003
- Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegansNature, 2002
- Clustering of housekeeping genes provides a unified model of gene order in the human genomeNature Genetics, 2002
- MIPS: a database for genomes and protein sequencesNucleic Acids Research, 2002
- PharmGKB: the Pharmacogenetics Knowledge BaseNucleic Acids Research, 2002
- Gene Ontology: tool for the unification of biologyNature Genetics, 2000
- Systematic determination of genetic network architectureNature Genetics, 1999