Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics.
Identifieur interne : 002E33 ( Main/Exploration ); précédent : 002E32; suivant : 002E34Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics.
Auteurs : Xiaohan Yang [États-Unis] ; Chu-Yu Ye ; Anjali Bisaria ; Gerald A. Tuskan ; Udaya C. KalluriSource :
- Plant science : an international journal of experimental plant biology [ 1873-2259 ] ; 2011.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Arabidopsis, Populus, Voies de biosynthèse.
- métabolisme : Arabidopsis, Paroi cellulaire, Populus.
- Biocarburants, Biomasse, Expression des gènes, Fouille de données, Gènes de plante, Génomique.
English descriptors
- KwdEn :
- MESH :
- chemical : Biofuels.
- genetics : Arabidopsis, Biosynthetic Pathways, Populus.
- metabolism : Arabidopsis, Cell Wall, Populus.
- Biomass, Data Mining, Gene Expression, Genes, Plant, Genomics.
Abstract
Populus is an important bioenergy crop for bioethanol production. A greater understanding of cell wall biosynthesis processes is critical in reducing biomass recalcitrance, a major hindrance in efficient generation of biofuels from lignocellulosic biomass. Here, we report the identification of candidate cell wall biosynthesis genes through the development and application of a novel bioinformatics pipeline. As a first step, via text-mining of PubMed publications, we obtained 121 Arabidopsis genes that had the experimental evidence supporting their involvement in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database, and additional genes were identified as neighbors of the bait genes in the network, increasing the number of genes to 548. The 548 Arabidopsis genes were then used to re-query the Arabidopsis co-expression database and re-construct a network that captured additional network neighbors, expanding to a total of 694 genes. The 694 Arabidopsis genes were computationally divided into 22 clusters. Queries of the Populus genome using the Arabidopsis genes revealed 817 Populus orthologs. Functional analysis of gene ontology and tissue-specific gene expression indicated that these Arabidopsis and Populus genes are high likelihood candidates for functional characterization in relation to cell wall biosynthesis.
DOI: 10.1016/j.plantsci.2011.01.020
PubMed: 21958710
Affiliations:
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Tuskan</name></author><author><name sortKey="Kalluri, Udaya C" sort="Kalluri, Udaya C" uniqKey="Kalluri U" first="Udaya C" last="Kalluri">Udaya C. 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Kalluri</name></author></analytic><series><title level="j">Plant science : an international journal of experimental plant biology</title><idno type="eISSN">1873-2259</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Arabidopsis (metabolism)</term><term>Biofuels (MeSH)</term><term>Biomass (MeSH)</term><term>Biosynthetic Pathways (genetics)</term><term>Cell Wall (metabolism)</term><term>Data Mining (MeSH)</term><term>Gene Expression (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genomics (MeSH)</term><term>Populus (genetics)</term><term>Populus (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Arabidopsis (génétique)</term><term>Arabidopsis (métabolisme)</term><term>Biocarburants (MeSH)</term><term>Biomasse (MeSH)</term><term>Expression des gènes (MeSH)</term><term>Fouille de données (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génomique (MeSH)</term><term>Paroi cellulaire (métabolisme)</term><term>Populus (génétique)</term><term>Populus (métabolisme)</term><term>Voies de biosynthèse (génétique)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Biofuels</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Biosynthetic Pathways</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Populus</term><term>Voies de biosynthèse</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Arabidopsis</term><term>Cell Wall</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Arabidopsis</term><term>Paroi cellulaire</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biomass</term><term>Data Mining</term><term>Gene Expression</term><term>Genes, Plant</term><term>Genomics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Biocarburants</term><term>Biomasse</term><term>Expression des gènes</term><term>Fouille de données</term><term>Gènes de plante</term><term>Génomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Populus is an important bioenergy crop for bioethanol production. A greater understanding of cell wall biosynthesis processes is critical in reducing biomass recalcitrance, a major hindrance in efficient generation of biofuels from lignocellulosic biomass. Here, we report the identification of candidate cell wall biosynthesis genes through the development and application of a novel bioinformatics pipeline. As a first step, via text-mining of PubMed publications, we obtained 121 Arabidopsis genes that had the experimental evidence supporting their involvement in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database, and additional genes were identified as neighbors of the bait genes in the network, increasing the number of genes to 548. The 548 Arabidopsis genes were then used to re-query the Arabidopsis co-expression database and re-construct a network that captured additional network neighbors, expanding to a total of 694 genes. The 694 Arabidopsis genes were computationally divided into 22 clusters. Queries of the Populus genome using the Arabidopsis genes revealed 817 Populus orthologs. Functional analysis of gene ontology and tissue-specific gene expression indicated that these Arabidopsis and Populus genes are high likelihood candidates for functional characterization in relation to cell wall biosynthesis.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21958710</PMID><DateCompleted><Year>2012</Year><Month>01</Month><Day>23</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1873-2259</ISSN><JournalIssue CitedMedium="Internet"><Volume>181</Volume><Issue>6</Issue><PubDate><Year>2011</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Plant science : an international journal of experimental plant biology</Title><ISOAbbreviation>Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics.</ArticleTitle><Pagination><MedlinePgn>675-87</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.plantsci.2011.01.020</ELocationID><Abstract><AbstractText>Populus is an important bioenergy crop for bioethanol production. A greater understanding of cell wall biosynthesis processes is critical in reducing biomass recalcitrance, a major hindrance in efficient generation of biofuels from lignocellulosic biomass. Here, we report the identification of candidate cell wall biosynthesis genes through the development and application of a novel bioinformatics pipeline. As a first step, via text-mining of PubMed publications, we obtained 121 Arabidopsis genes that had the experimental evidence supporting their involvement in cell wall biosynthesis or remodeling. The 121 genes were then used as bait genes to query an Arabidopsis co-expression database, and additional genes were identified as neighbors of the bait genes in the network, increasing the number of genes to 548. The 548 Arabidopsis genes were then used to re-query the Arabidopsis co-expression database and re-construct a network that captured additional network neighbors, expanding to a total of 694 genes. 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Kalluri</name><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name><name sortKey="Ye, Chu Yu" sort="Ye, Chu Yu" uniqKey="Ye C" first="Chu-Yu" last="Ye">Chu-Yu Ye</name></noCountry><country name="États-Unis"><region name="Tennessee"><name sortKey="Yang, Xiaohan" sort="Yang, Xiaohan" uniqKey="Yang X" first="Xiaohan" last="Yang">Xiaohan Yang</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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