Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics
Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.
| Veröffentlicht in: | Plant science : an international journal of experimental plant biology. - 1985. - 181(2011), 6 vom: 06. Dez., Seite 675-87 |
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| 1. Verfasser: | |
| Weitere Verfasser: | , , , |
| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2011
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| Zugriff auf das übergeordnete Werk: | Plant science : an international journal of experimental plant biology |
| Schlagworte: | Comparative Study Journal Article Research Support, U.S. Gov't, Non-P.H.S. Biofuels |
| Zusammenfassung: | Copyright © 2011 Elsevier Ireland Ltd. All rights reserved. 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 |
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| Beschreibung: | Date Completed 23.01.2012 Date Revised 11.03.2022 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1873-2259 |
| DOI: | 10.1016/j.plantsci.2011.01.020 |