ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics
1 Seoul National University Biomedical Informatics (SNUBI) and 2 Human Genome Research Institute, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
* To whom correspondence should be addressed at. Tel: +82 27408320; Fax: +82 7474830; Email: juhan{at}snu.ac.kr
Received February 15, 2004; Revised April 18, 2004; Accepted May 3, 2004
Biological pathways can provide key information on the organization of biological systems. ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG). By integrating major bio-databases and searching pathway resources, ArrayXPath automatically maps different types of identifiers from microarray probes and pathway elements. When one inputs gene-expression clusters, ArrayXPath produces a list of the best matching pathways for each cluster. We applied Fisher's exact test and the false discovery rate (FDR) to evaluate the statistical significance of the association between a cluster and a pathway while correcting the multiple-comparison problem. ArrayXPath produces Javascript-enabled SVGs for web-enabled interactive visualization of pathways integrated with gene-expression profiles.
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