The MORPH-R web server and software tool for predicting missing genes in biological pathways

David Amar; Itziar Frades; Tim Diels; David Zaltzman; Netanel Ghatan; Pete E Hedley; Erik Alexandersson; Oren Tzfadia; Ron Shamir

doi:10.1111/ppl.12326

The MORPH-R web server and software tool for predicting missing genes in biological pathways

David Amar, Itziar Frades, Tim Diels, David Zaltzman, Netanel Ghatan, Pete E Hedley, Erik Alexandersson, Oren Tzfadia, Ron Shamir

Mycobacteriology

Research output: Contribution to journal › A1: Web of Science-article › peer-review

Abstract

A biological pathway is the set of molecular entities involved in a given biological process and the interrelations among them. Even though biological pathways have been studied extensively, discovering missing genes in pathways remains a fundamental challenge. Here, we present an easy-to-use tool that allows users to run MORPH (MOdule-guided Ranking of candidate PatHway genes), an algorithm for revealing missing genes in biological pathways, and demonstrate its capabilities. MORPH supports the analysis in tomato, Arabidopsis and the two new species: rice and the newly sequenced potato genome. The new tool, called MORPH-R, is available both as a web server (at http://bioinformatics.psb.ugent.be/webtools/morph/) and as standalone software that can be used locally. In the standalone version, the user can apply the tool to new organisms using any proprietary and public data sources.

Original language	English
Journal	Physiologia Plantarum
Volume	155
Issue number	1
Pages (from-to)	12-20
Number of pages	9
ISSN	0031-9317
DOIs	https://doi.org/10.1111/ppl.12326
Publication status	Published - 2015

Keywords

Algorithms
Arabidopsis/genetics
Biosynthetic Pathways/genetics
Computational Biology/methods
Gene Ontology
Genes, Plant/genetics
Internet
Lycopersicon esculentum/genetics
Oryza/genetics
Reproducibility of Results
Software
Solanum tuberosum/genetics

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10.1111/ppl.12326

Cite this

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title = "The MORPH-R web server and software tool for predicting missing genes in biological pathways",

abstract = "A biological pathway is the set of molecular entities involved in a given biological process and the interrelations among them. Even though biological pathways have been studied extensively, discovering missing genes in pathways remains a fundamental challenge. Here, we present an easy-to-use tool that allows users to run MORPH (MOdule-guided Ranking of candidate PatHway genes), an algorithm for revealing missing genes in biological pathways, and demonstrate its capabilities. MORPH supports the analysis in tomato, Arabidopsis and the two new species: rice and the newly sequenced potato genome. The new tool, called MORPH-R, is available both as a web server (at http://bioinformatics.psb.ugent.be/webtools/morph/) and as standalone software that can be used locally. In the standalone version, the user can apply the tool to new organisms using any proprietary and public data sources. ",

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author = "David Amar and Itziar Frades and Tim Diels and David Zaltzman and Netanel Ghatan and Hedley, {Pete E} and Erik Alexandersson and Oren Tzfadia and Ron Shamir",

note = "{\textcopyright} 2015 Scandinavian Plant Physiology Society.",

year = "2015",

doi = "10.1111/ppl.12326",

language = "English",

volume = "155",

pages = "12--20",

journal = "Physiologia Plantarum",

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TY - JOUR

T1 - The MORPH-R web server and software tool for predicting missing genes in biological pathways

AU - Amar, David

AU - Frades, Itziar

AU - Diels, Tim

AU - Zaltzman, David

AU - Ghatan, Netanel

AU - Hedley, Pete E

AU - Alexandersson, Erik

AU - Tzfadia, Oren

AU - Shamir, Ron

PY - 2015

Y1 - 2015

N2 - A biological pathway is the set of molecular entities involved in a given biological process and the interrelations among them. Even though biological pathways have been studied extensively, discovering missing genes in pathways remains a fundamental challenge. Here, we present an easy-to-use tool that allows users to run MORPH (MOdule-guided Ranking of candidate PatHway genes), an algorithm for revealing missing genes in biological pathways, and demonstrate its capabilities. MORPH supports the analysis in tomato, Arabidopsis and the two new species: rice and the newly sequenced potato genome. The new tool, called MORPH-R, is available both as a web server (at http://bioinformatics.psb.ugent.be/webtools/morph/) and as standalone software that can be used locally. In the standalone version, the user can apply the tool to new organisms using any proprietary and public data sources.

AB - A biological pathway is the set of molecular entities involved in a given biological process and the interrelations among them. Even though biological pathways have been studied extensively, discovering missing genes in pathways remains a fundamental challenge. Here, we present an easy-to-use tool that allows users to run MORPH (MOdule-guided Ranking of candidate PatHway genes), an algorithm for revealing missing genes in biological pathways, and demonstrate its capabilities. MORPH supports the analysis in tomato, Arabidopsis and the two new species: rice and the newly sequenced potato genome. The new tool, called MORPH-R, is available both as a web server (at http://bioinformatics.psb.ugent.be/webtools/morph/) and as standalone software that can be used locally. In the standalone version, the user can apply the tool to new organisms using any proprietary and public data sources.

KW - Algorithms

KW - Arabidopsis/genetics

KW - Biosynthetic Pathways/genetics

KW - Computational Biology/methods

KW - Gene Ontology

KW - Genes, Plant/genetics

KW - Internet

KW - Lycopersicon esculentum/genetics

KW - Oryza/genetics

KW - Reproducibility of Results

KW - Software

KW - Solanum tuberosum/genetics

U2 - 10.1111/ppl.12326

DO - 10.1111/ppl.12326

M3 - A1: Web of Science-article

C2 - 25625434

SN - 0031-9317

VL - 155

SP - 12

EP - 20

JO - Physiologia Plantarum

JF - Physiologia Plantarum

IS - 1

ER -

The MORPH-R web server and software tool for predicting missing genes in biological pathways

Abstract

Keywords

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