Novel function discovery with GeneMANIA:: a new integrated resource for gene function prediction in Escherichia coli

James Vlasblom; Khalid Zuberi; Harold Rodriguez; Roland Arnold; Alla Gagarinova; Viktor Deineko; Ashwani Kumar; Elisa Leung; Kamran Rizzolo; Bahram Samanfar; Luke Chang; Sadhna Phanse; Ashkan Golshani; Jack F Greenblatt; Walid A Houry; Andrew Emili; Quaid Morris; Gary Bader; Mohan Babu

doi:10.1093/bioinformatics/btu671

Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli

James Vlasblom, Khalid Zuberi, Harold Rodriguez, Roland Arnold, Alla Gagarinova, Viktor Deineko, Ashwani Kumar, Elisa Leung, Kamran Rizzolo, Bahram Samanfar, Luke Chang, Sadhna Phanse, Ashkan Golshani, Jack F Greenblatt, Walid A Houry, Andrew Emili, Quaid Morris, Gary Bader, Mohan Babu

Cancer and Genomic Sciences

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

28 Citations (Scopus)

Abstract

MOTIVATION: The model bacterium Escherichia coli is among the best studied prokaryotes, yet nearly half of its proteins are still of unknown biological function. This is despite a wealth of available large-scale physical and genetic interaction data. To address this, we extended the GeneMANIA function prediction web application developed for model eukaryotes to support E.coli.

RESULTS: We integrated 48 distinct E.coli functional interaction datasets and used the GeneMANIA algorithm to produce thousands of novel functional predictions and prioritize genes for further functional assays. Our analysis achieved cross-validation performance comparable to that reported for eukaryotic model organisms, and revealed new functions for previously uncharacterized genes in specific bioprocesses, including components required for cell adhesion, iron-sulphur complex assembly and ribosome biogenesis. The GeneMANIA approach for network-based function prediction provides an innovative new tool for probing mechanisms underlying bacterial bioprocesses.

CONTACT: gary.bader@utoronto.ca; mohan.babu@uregina.ca

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original language	English
Pages (from-to)	306-310
Number of pages	5
Journal	Bioinformatics
Volume	31
Issue number	3
DOIs	https://doi.org/10.1093/bioinformatics/btu671
Publication status	Published - 13 Oct 2014

Keywords

Algorithms
Escherichia coli
Escherichia coli Proteins
Gene Regulatory Networks
Phenotype
Software
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

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https://academic.oup.com/bioinformatics/article/31/3/306/2366256Licence: None: All rights reserved

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Vlasblom, J., Zuberi, K., Rodriguez, H., Arnold, R., Gagarinova, A., Deineko, V., Kumar, A., Leung, E., Rizzolo, K., Samanfar, B., Chang, L., Phanse, S., Golshani, A., Greenblatt, J. F., Houry, W. A., Emili, A., Morris, Q., Bader, G., & Babu, M. (2014). Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. Bioinformatics, 31(3), 306-310. https://doi.org/10.1093/bioinformatics/btu671

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title = "Novel function discovery with GeneMANIA:: a new integrated resource for gene function prediction in Escherichia coli",

abstract = "MOTIVATION: The model bacterium Escherichia coli is among the best studied prokaryotes, yet nearly half of its proteins are still of unknown biological function. This is despite a wealth of available large-scale physical and genetic interaction data. To address this, we extended the GeneMANIA function prediction web application developed for model eukaryotes to support E.coli.RESULTS: We integrated 48 distinct E.coli functional interaction datasets and used the GeneMANIA algorithm to produce thousands of novel functional predictions and prioritize genes for further functional assays. Our analysis achieved cross-validation performance comparable to that reported for eukaryotic model organisms, and revealed new functions for previously uncharacterized genes in specific bioprocesses, including components required for cell adhesion, iron-sulphur complex assembly and ribosome biogenesis. The GeneMANIA approach for network-based function prediction provides an innovative new tool for probing mechanisms underlying bacterial bioprocesses.CONTACT: gary.bader@utoronto.ca; mohan.babu@uregina.caSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.",

keywords = "Algorithms, Escherichia coli, Escherichia coli Proteins, Gene Regulatory Networks, Phenotype, Software, Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't",

author = "James Vlasblom and Khalid Zuberi and Harold Rodriguez and Roland Arnold and Alla Gagarinova and Viktor Deineko and Ashwani Kumar and Elisa Leung and Kamran Rizzolo and Bahram Samanfar and Luke Chang and Sadhna Phanse and Ashkan Golshani and Greenblatt, {Jack F} and Houry, {Walid A} and Andrew Emili and Quaid Morris and Gary Bader and Mohan Babu",

year = "2014",

month = oct,

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doi = "10.1093/bioinformatics/btu671",

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Vlasblom, J, Zuberi, K, Rodriguez, H, Arnold, R, Gagarinova, A, Deineko, V, Kumar, A, Leung, E, Rizzolo, K, Samanfar, B, Chang, L, Phanse, S, Golshani, A, Greenblatt, JF, Houry, WA, Emili, A, Morris, Q, Bader, G & Babu, M 2014, 'Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli', Bioinformatics, vol. 31, no. 3, pp. 306-310. https://doi.org/10.1093/bioinformatics/btu671

TY - JOUR

T1 - Novel function discovery with GeneMANIA:

T2 - a new integrated resource for gene function prediction in Escherichia coli

AU - Vlasblom, James

AU - Zuberi, Khalid

AU - Rodriguez, Harold

AU - Arnold, Roland

AU - Gagarinova, Alla

AU - Deineko, Viktor

AU - Kumar, Ashwani

AU - Leung, Elisa

AU - Rizzolo, Kamran

AU - Samanfar, Bahram

AU - Chang, Luke

AU - Phanse, Sadhna

AU - Golshani, Ashkan

AU - Greenblatt, Jack F

AU - Houry, Walid A

AU - Emili, Andrew

AU - Morris, Quaid

AU - Bader, Gary

AU - Babu, Mohan

PY - 2014/10/13

Y1 - 2014/10/13

N2 - MOTIVATION: The model bacterium Escherichia coli is among the best studied prokaryotes, yet nearly half of its proteins are still of unknown biological function. This is despite a wealth of available large-scale physical and genetic interaction data. To address this, we extended the GeneMANIA function prediction web application developed for model eukaryotes to support E.coli.RESULTS: We integrated 48 distinct E.coli functional interaction datasets and used the GeneMANIA algorithm to produce thousands of novel functional predictions and prioritize genes for further functional assays. Our analysis achieved cross-validation performance comparable to that reported for eukaryotic model organisms, and revealed new functions for previously uncharacterized genes in specific bioprocesses, including components required for cell adhesion, iron-sulphur complex assembly and ribosome biogenesis. The GeneMANIA approach for network-based function prediction provides an innovative new tool for probing mechanisms underlying bacterial bioprocesses.CONTACT: gary.bader@utoronto.ca; mohan.babu@uregina.caSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AB - MOTIVATION: The model bacterium Escherichia coli is among the best studied prokaryotes, yet nearly half of its proteins are still of unknown biological function. This is despite a wealth of available large-scale physical and genetic interaction data. To address this, we extended the GeneMANIA function prediction web application developed for model eukaryotes to support E.coli.RESULTS: We integrated 48 distinct E.coli functional interaction datasets and used the GeneMANIA algorithm to produce thousands of novel functional predictions and prioritize genes for further functional assays. Our analysis achieved cross-validation performance comparable to that reported for eukaryotic model organisms, and revealed new functions for previously uncharacterized genes in specific bioprocesses, including components required for cell adhesion, iron-sulphur complex assembly and ribosome biogenesis. The GeneMANIA approach for network-based function prediction provides an innovative new tool for probing mechanisms underlying bacterial bioprocesses.CONTACT: gary.bader@utoronto.ca; mohan.babu@uregina.caSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

KW - Algorithms

KW - Escherichia coli

KW - Escherichia coli Proteins

KW - Gene Regulatory Networks

KW - Phenotype

KW - Software

KW - Journal Article

KW - Research Support, N.I.H., Extramural

KW - Research Support, Non-U.S. Gov't

U2 - 10.1093/bioinformatics/btu671

DO - 10.1093/bioinformatics/btu671

M3 - Article

C2 - 25316676

SN - 1367-4803

VL - 31

SP - 306

EP - 310

JO - Bioinformatics

JF - Bioinformatics

IS - 3

ER -

Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli

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Keywords

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