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Sci. Signal., 5 August 2008
Vol. 1, Issue 31, p. pt4
[DOI: 10.1126/scisignal.131pt4]


pathFinder: A Static Network Analysis Tool for Pharmacological Analysis of Signal Transduction Pathways

Babru B. Samal1* and Lee E. Eiden2

1National Institute of Mental Health—Intramural Research Programs (NIMH-IRP) Bioinformatics Core, NIMH, NIH, Bethesda, MD 20892, USA.
2Section on Molecular Neuroscience, Laboratory of Cellular and Molecular Regulation, 9000 Rockville Pike, Building 49, Room 5A-68, NIH, Bethesda, MD 20892, USA.

A presentation from the Experimental Biology 2008 Meeting, San Diego, California, USA, 5 to 9 April 2008

Abstract: The study of signal transduction is becoming a de facto part of the analysis of gene expression and protein profiling techniques. Many online tools are used to cluster genes in various ways or to assign gene products to signal transduction pathways. Among these, pathFinder is a unique tool that can find signal transduction pathways between first, second, or nth messengers and their targets within the cell. pathFinder can identify qualitatively all possible signal transduction pathways connecting any starting component and target within a database of two-component pathways (directional dyads). One or more intermediate pathway components can be excluded to simulate the use of pharmacological inhibitors or genetic deletion (knockout). Missing elements in a pathway connecting the activator or initiator and target can also be inferred from a null pathway result. The value of this static network analysis tool is illustrated by the predication from pathFinder analysis of a novel cyclic AMP–dependent, protein kinase A–independent signaling pathway in neuroendocrine cells, which has been experimentally confirmed.

*Presenter and corresponding author. E-mail: samalb{at}

Citation: B. B. Samal, L. E. Eiden, pathFinder: A Static Network Analysis Tool for Pharmacological Analysis of Signal Transduction Pathways. Sci. Signal. 1, pt4 (2008).

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