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Sci. Signal., 25 October 2011
Vol. 4, Issue 196, p. pl1
[DOI: 10.1126/scisignal.2001935]

PROTOCOLS

ANAT: A Tool for Constructing and Analyzing Functional Protein Networks

Nir Yosef1,2, Einat Zalckvar3, Assaf D. Rubinstein3, Max Homilius4, Nir Atias5, Liram Vardi5, Igor Berman5, Hadas Zur5, Adi Kimchi3, Eytan Ruppin5,6, and Roded Sharan5*

1 Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
2 Center for Neurologic Diseases, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA.
3 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
4 Institute of Computer Science, Freie Universität Berlin, Takustr. 9, D-14195 Berlin, Germany.
5 Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel.
6 School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel.

Abstract: Genome-scale screening studies are gradually accumulating a wealth of data on the putative involvement of hundreds of genes in various cellular responses or functions. A fundamental challenge is to chart the molecular pathways that underlie these systems. ANAT is an interactive software tool, implemented as a Cytoscape plug-in, for elucidating functional networks of proteins. It encompasses a number of network inference algorithms and provides access to networks of physical associations in several organisms. In contrast to existing software tools, ANAT can be used to infer subnetworks that connect hundreds of proteins to each other or to a given set of "anchor" proteins, a fundamental step in reconstructing cellular subnetworks. The interactive component of ANAT provides an array of tools for evaluating and exploring the resulting subnetwork models and for iteratively refining them. We demonstrate the utility of ANAT by studying the crosstalk between the autophagic and apoptotic cell death modules in humans, using a network of physical interactions. Relative to published software tools, ANAT is more accurate and provides more features for comprehensive network analysis. The latest version of the software is available at http://www.cs.tau.ac.il/~bnet/ANAT_SI.

*Corresponding author. E-mail, roded{at}post.tau.ac.il

Citation: N. Yosef, E. Zalckvar, A. D. Rubinstein, M. Homilius, N. Atias, L. Vardi, I. Berman, H. Zur, A. Kimchi, E. Ruppin, R. Sharan, ANAT: A Tool for Constructing and Analyzing Functional Protein Networks. Sci. Signal. 4, pl1 (2011).

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