HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) All Versions of this Article: M400039-MCP200v1 3/10/1009    most recent Submit a response Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Request Permissions Glossary Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Paek, E. Articles by Lee, K.-J. Search for Related Content PubMed PubMed Citation Articles by Paek, E. Articles by Lee, K.-J. Social Bookmarking                      What's this?

Molecular & Cellular Proteomics 3:1009-1022, 2004.
© 2004 by The American Society for Biochemistry and Molecular Biology, Inc.

---

Research

Multi-layered Representation for Cell Signaling Pathways^*

Eunok Paek^,, Jisook Park^¶ and Kong-Joo Lee^||,

From the Department of Mechanical and Information Engineering, University of Seoul, Seoul 130-743, Republic of Korea; ^¶ Division of Information and Communication Engineering, Seoul Women’s University, Seoul 139-774, Republic of Korea; and ^|| Center for Cell Signaling Research, Division of Molecular Life Sciences & College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea

To understand complex signaling pathways and networks, it is necessary to develop a formal and structured representation of the available information in a format suitable for analysis by software tools. Due to the complexity and incompleteness of the current biological knowledge about cell signaling, such a device must be able to represent cellular pathways at differing levels of details, one level of information abstract enough to convey an essential signaling flow while hiding its details and another level of information detailed enough to explain the underlying mechanisms that account for the signaling flow described at a more abstract level. We have defined a formal ontology for cell-signaling events that allows us to describe these cellular pathways at various levels of abstraction. Using this formal representation, ROSPath (reactive oxygen species-mediated signaling pathway) database system has been implemented and made available on the web (rospath.ewha.ac.kr). ROSPath is a database system for reactive oxygen species (ROS)-mediated cell signaling pathways and signaling processes in molecular detail, which facilitates a comprehensive understanding of the regulatory mechanisms in signaling pathways. ROSPath includes growth factor-, stress-, and cytokine-induced signaling pathways containing about 500 unique proteins (mostly mammalian) and their related protein states, protein complexes, protein complex states, signaling interactions, signaling steps, and pathways. It is a web-based structured repository of information on the signaling pathways of interest and provides a means for managing data produced by large-scale and high-throughput techniques such as proteomics. Also, software tools are provided for querying, displaying, and analyzing pathways, thus furnishing an integrated web environment for visualizing and manipulating ROS-mediated cell-signaling events.

CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				M. Suderman and M. Hallett Tools for visually exploring biological networks Bioinformatics, October 15, 2007; 23(20): 2651 - 2659. [Abstract] [Full Text] [PDF]