Skip Navigation

Nucleic Acids Research 2005 33(Web Server Issue):W621-W626; doi:10.1093/nar/gki450
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1228K) Freely available
Right arrow Screen PDF (352K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Chung, H.-J.
Right arrow Articles by Kim, J. H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Chung, H.-J.
Right arrow Articles by Kim, J. H.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

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

Hee-Joon Chung1, Chan Hee Park1, Mi Ryung Han1, Seokho Lee1, Jung Hun Ohn1, Jihoon Kim1, Jihun Kim1 and Ju Han Kim1,2,*

1Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine Seoul 110-799, Korea 2Human Genome Research Institute, Seoul National University College of Medicine Seoul 110-799, Korea

*To whom correspondence should be addressed. Tel: +82 2 740 8320; Fax: +82 2 742 5947; Email: juhan{at}snu.ac.kr

Received February 13, 2005. Revised March 31, 2005. Accepted March 31, 2005.

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
C. Li, X. Li, Y. Miao, Q. Wang, W. Jiang, C. Xu, J. Li, J. Han, F. Zhang, B. Gong, et al.
SubpathwayMiner: a software package for flexible identification of pathways
Nucleic Acids Res., October 1, 2009; 37(19): e131 - e131.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Goffard, T. Frickey, and G. Weiller
PathExpress update: the enzyme neighbourhood method of associating gene-expression data with metabolic pathways
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W335 - W339.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. Frijters, B. Heupers, P. van Beek, M. Bouwhuis, R. van Schaik, J. de Vlieg, J. Polman, and W. Alkema
CoPub: a literature-based keyword enrichment tool for microarray data analysis
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W406 - W410.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. Segota, N. Bartonicek, and K. Vlahovicek
MADNet: microarray database network web server
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W332 - W335.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Nam, B. Kim, S. Shin, and S. Lee
miRGator: an integrated system for functional annotation of microRNAs
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D159 - D164.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Goffard and G. Weiller
PathExpress: a web-based tool to identify relevant pathways in gene expression data
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W176 - W181.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Z. Hu, D. M. Ng, T. Yamada, C. Chen, S. Kawashima, J. Mellor, B. Linghu, M. Kanehisa, J. M. Stuart, and C. DeLisi
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W625 - W632.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.