ANAT: a tool for constructing and analyzing functional protein networks.
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.
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
Nir
N
Yosef
Einat
E
Zalckvar
Assaf D
AD
Rubinstein
Max
M
Homilius
Nir
N
Atias
Liram
L
Vardi
Igor
I
Berman
Hadas
H
Zur
Adi
A
Kimchi
Eytan
E
Ruppin
Roded
R
Sharan
D000465:Algorithms; D000818:Animals; D017209:Apoptosis / Q000235:genetics / Q000502:physiology; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D001343:Autophagy / Q000235:genetics / Q000502:physiology; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism; D004331:Drosophila melanogaster / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D016678:Genome / Q000235:genetics; D016480:Helicobacter pylori / Q000235:genetics / Q000378:metabolism; D006801:Humans; D020407:Internet; D051379:Mice; D008954:Models, Biological; D010963:Plasmodium falciparum / Q000235:genetics / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000235:genetics / Q000378:metabolism*; D051381:Rats; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology*; D012984:Software
D011506:Proteins