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MorphDB : prioritizing genes for specialized metabolism pathways and gene ontology categories in plants

Arthur Zwaenepoel UGent, Tim Diels, David Amar, Thomas Van Parys UGent, Ron Shamir, Yves Van de Peer UGent and Oren Tzfadia UGent (2018) FRONTIERS IN PLANT SCIENCE. 9.
abstract
Recent times have seen an enormous growth of "omics" data, of which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for the functional classification of gene sequences, common similarity-based methods often fall short of providing full and reliable functional information. Recently, the combination of comparative genomics with approaches in functional genomics has received considerable interest for gene function analysis, leveraging both gene expression based guilt-by-association methods and annotation efforts in closely related model organisms. Besides the identification of missing genes in pathways, these methods also typically enable the discovery of biological regulators (i.e., transcription factors or signaling genes). A previously built guilt-by-association method is MORPH, which was proven to be an efficient algorithm that performs particularly well in identifying and prioritizing missing genes in plant metabolic pathways. Here, we present MorphDB, a resource where MORPH-based candidate genes for large-scale functional annotations (Gene Ontology, MapMan bins) are integrated across multiple plant species. Besides a gene centric query utility, we present a comparative network approach that enables researchers to efficiently browse MORPH predictions across functional gene sets and species, facilitating efficient gene discovery and candidate gene prioritization. MorphDB is available at http://bioinformatics.psb.ugent.be/webtools/morphdb/morphDB/index/. We also provide a toolkit, named "MORPH bulk" (https://github.com/arzwa/morph-bulk), for running MORPH in bulk mode on novel data sets, enabling researchers to apply MORPH to their own species of interest.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
ELEMENT-BINDING FACTORS, TURNIP CRINKLE VIRUS, TRANSCRIPTION FACTOR, ARABIDOPSIS-THALIANA, PHENYLPROPANOID METABOLISM, CATHARANTHUS-ROSEUS, SALICYLIC-ACID, GENOME, EXPRESSION, INTEGRATION, comparative co-expression networks, candidate gene prioritization, functional annotation, MORPH, defense response
journal title
FRONTIERS IN PLANT SCIENCE
Front. Plant Sci.
volume
9
article number
352
pages
13 pages
Web of Science type
Article
Web of Science id
000427707500001
ISSN
1664-462X
DOI
10.3389/fpls.2018.00352
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
8558237
handle
http://hdl.handle.net/1854/LU-8558237
date created
2018-04-03 14:15:09
date last changed
2018-06-05 09:22:54
@article{8558237,
  abstract     = {Recent times have seen an enormous growth of {\textacutedbl}omics{\textacutedbl} data, of which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for the functional classification of gene sequences, common similarity-based methods often fall short of providing full and reliable functional information. Recently, the combination of comparative genomics with approaches in functional genomics has received considerable interest for gene function analysis, leveraging both gene expression based guilt-by-association methods and annotation efforts in closely related model organisms. Besides the identification of missing genes in pathways, these methods also typically enable the discovery of biological regulators (i.e., transcription factors or signaling genes). A previously built guilt-by-association method is MORPH, which was proven to be an efficient algorithm that performs particularly well in identifying and prioritizing missing genes in plant metabolic pathways. Here, we present MorphDB, a resource where MORPH-based candidate genes for large-scale functional annotations (Gene Ontology, MapMan bins) are integrated across multiple plant species. Besides a gene centric query utility, we present a comparative network approach that enables researchers to efficiently browse MORPH predictions across functional gene sets and species, facilitating efficient gene discovery and candidate gene prioritization. MorphDB is available at http://bioinformatics.psb.ugent.be/webtools/morphdb/morphDB/index/. We also provide a toolkit, named {\textacutedbl}MORPH bulk{\textacutedbl} (https://github.com/arzwa/morph-bulk), for running MORPH in bulk mode on novel data sets, enabling researchers to apply MORPH to their own species of interest.},
  articleno    = {352},
  author       = {Zwaenepoel, Arthur and Diels, Tim and Amar, David and Van Parys, Thomas and Shamir, Ron and Van de Peer, Yves and Tzfadia, Oren},
  issn         = {1664-462X},
  journal      = {FRONTIERS IN PLANT SCIENCE},
  keyword      = {ELEMENT-BINDING FACTORS,TURNIP CRINKLE VIRUS,TRANSCRIPTION FACTOR,ARABIDOPSIS-THALIANA,PHENYLPROPANOID METABOLISM,CATHARANTHUS-ROSEUS,SALICYLIC-ACID,GENOME,EXPRESSION,INTEGRATION,comparative co-expression networks,candidate gene prioritization,functional annotation,MORPH,defense response},
  language     = {eng},
  pages        = {13},
  title        = {MorphDB : prioritizing genes for specialized metabolism pathways and gene ontology categories in plants},
  url          = {http://dx.doi.org/10.3389/fpls.2018.00352},
  volume       = {9},
  year         = {2018},
}

Chicago
Zwaenepoel, Arthur, Tim Diels, David Amar, Thomas Van Parys, Ron Shamir, Yves Van de Peer, and Oren Tzfadia. 2018. “MorphDB : Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants.” Frontiers in Plant Science 9.
APA
Zwaenepoel, Arthur, Diels, T., Amar, D., Van Parys, T., Shamir, R., Van de Peer, Y., & Tzfadia, O. (2018). MorphDB : prioritizing genes for specialized metabolism pathways and gene ontology categories in plants. FRONTIERS IN PLANT SCIENCE, 9.
Vancouver
1.
Zwaenepoel A, Diels T, Amar D, Van Parys T, Shamir R, Van de Peer Y, et al. MorphDB : prioritizing genes for specialized metabolism pathways and gene ontology categories in plants. FRONTIERS IN PLANT SCIENCE. 2018;9.
MLA
Zwaenepoel, Arthur, Tim Diels, David Amar, et al. “MorphDB : Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants.” FRONTIERS IN PLANT SCIENCE 9 (2018): n. pag. Print.