ANAT 2.0: Reconstructing functional protein subnetworks

Yomtov Almozlino; Nir Atias; Dana Silverbush; Roded Sharan

doi:10.1186/s12859-017-1932-1

ANAT 2.0: Reconstructing functional protein subnetworks

Yomtov Almozlino, Nir Atias, Dana Silverbush, Roded Sharan

School of Computer Science

Tel Aviv University

Research output: Contribution to journal › Article › peer-review

Abstract

Background: ANAT is a graphical, Cytoscape-based tool for the inference of protein networks that underlie a process of interest. The ANAT tool allows the user to perform network reconstruction under several scenarios in a number of organisms including yeast and human. Results: Here we report on a new version of the tool, ANAT 2.0, which introduces substantial code and database updates as well as several new network reconstruction algorithms that greatly extend the applicability of the tool to biological data sets. Conclusions: ANAT 2.0 is an up-to-date network reconstruction tool that addresses several reconstruction challenges across multiple species.

Original language	English
Article number	495
Journal	BMC Bioinformatics
Volume	18
Issue number	1
DOIs	https://doi.org/10.1186/s12859-017-1932-1
State	Published - 16 Nov 2017

Keywords

Cytoscape plugin
Network inference
Protein-protein interaction network
Subnetwork reconstruction

All Science Journal Classification (ASJC) codes

Structural Biology
Biochemistry
Molecular Biology
Computer Science Applications
Applied Mathematics

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10.1186/s12859-017-1932-1

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title = "ANAT 2.0: Reconstructing functional protein subnetworks",

abstract = "Background: ANAT is a graphical, Cytoscape-based tool for the inference of protein networks that underlie a process of interest. The ANAT tool allows the user to perform network reconstruction under several scenarios in a number of organisms including yeast and human. Results: Here we report on a new version of the tool, ANAT 2.0, which introduces substantial code and database updates as well as several new network reconstruction algorithms that greatly extend the applicability of the tool to biological data sets. Conclusions: ANAT 2.0 is an up-to-date network reconstruction tool that addresses several reconstruction challenges across multiple species.",

keywords = "Cytoscape plugin, Network inference, Protein-protein interaction network, Subnetwork reconstruction",

author = "Yomtov Almozlino and Nir Atias and Dana Silverbush and Roded Sharan",

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doi = "10.1186/s12859-017-1932-1",

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TY - JOUR

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T2 - Reconstructing functional protein subnetworks

AU - Almozlino, Yomtov

AU - Atias, Nir

AU - Silverbush, Dana

AU - Sharan, Roded

PY - 2017/11/16

Y1 - 2017/11/16

N2 - Background: ANAT is a graphical, Cytoscape-based tool for the inference of protein networks that underlie a process of interest. The ANAT tool allows the user to perform network reconstruction under several scenarios in a number of organisms including yeast and human. Results: Here we report on a new version of the tool, ANAT 2.0, which introduces substantial code and database updates as well as several new network reconstruction algorithms that greatly extend the applicability of the tool to biological data sets. Conclusions: ANAT 2.0 is an up-to-date network reconstruction tool that addresses several reconstruction challenges across multiple species.

AB - Background: ANAT is a graphical, Cytoscape-based tool for the inference of protein networks that underlie a process of interest. The ANAT tool allows the user to perform network reconstruction under several scenarios in a number of organisms including yeast and human. Results: Here we report on a new version of the tool, ANAT 2.0, which introduces substantial code and database updates as well as several new network reconstruction algorithms that greatly extend the applicability of the tool to biological data sets. Conclusions: ANAT 2.0 is an up-to-date network reconstruction tool that addresses several reconstruction challenges across multiple species.

KW - Cytoscape plugin

KW - Network inference

KW - Protein-protein interaction network

KW - Subnetwork reconstruction

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DO - 10.1186/s12859-017-1932-1

M3 - مقالة

SN - 1471-2105

VL - 18

JO - BMC Bioinformatics

JF - BMC Bioinformatics

IS - 1

M1 - 495

ER -

ANAT 2.0: Reconstructing functional protein subnetworks

Abstract

Keywords

All Science Journal Classification (ASJC) codes

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