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Large-scale mining co-expressed genes in Arabidopsis anther: From pair to group

Paper ID Volume ID Publish Year Pages File Format Full-Text
15231 1394 2011 7 PDF Available
Title
Large-scale mining co-expressed genes in Arabidopsis anther: From pair to group
Abstract

Research on gene co-expression not only plays an important role in understanding the complex regulatory relationships, but also contributes to our understanding of gene regulatory network. Beyond the co-expression knowledge between two genes, investigating the co-expression relationships among multiple target genes is more informative for understanding the basic working mechanisms in a cell. In this paper, all the Arabidopsis anther genes and every gene's potential co-expressed partners are collected by cross-database search. By combining simple pair gene co-expression networks, a complex Arabidopsis anther co-expression network is constructed. Maximum-clique algorithm is then applied to mine the groups reflecting co-expression relationships among multiple Arabidopsis anther genes that are represented by completely connected graphs. As a result, 254 Arabidopsis anther complete co-expression groups are obtained and our analysis shows that all the genes in the same group have high propensity to be functionally related and co-expressed together. We also demonstrate the efficacy of the proposed maximum-clique algorithm by comparing its results with the known Arabidopsis genome pathways, K-means clustering algorithm derived results and randomized data. It is expected that the 254 Arabidopsis anther complete co-expression groups generated in this paper can be a valuable knowledge source for further studies of molecular mechanisms of anther and its transcription regulations.

Graphical abstractResearch on gene co-expression not only plays an important role in understanding the complex regulatory relationships, but also contributes to our understanding of gene regulatory network. Beyond the co-expression knowledge between two genes, investigating the co-expression relationships among multiple target genes is more informative for understanding the basic working mechanisms in a cell. In this paper, all the Arabidopsis anther genes and every gene's potential co-expressed partners are collected by cross-database search. By combining simple pair gene co-expression networks, a complex Arabidopsis anther co-expression network is constructed. Maximum-clique algorithm is then applied to mine the groups reflecting co-expression relationships among multiple Arabidopsis anther genes that are represented by completely connected graphs. As a result, 254 Arabidopsis anther complete co-expression groups are obtained and our analysis shows that all the genes in the same group have high propensity to be functionally related and co-expressed together. We also demonstrate the efficacy of the proposed maximum-clique algorithm by comparing its results with the known Arabidopsis genome pathways, K-means clustering algorithm derived results and randomized data. It is expected that the 254 Arabidopsis anther complete co-expression groups generated in this paper can be a valuable knowledge source for further studies of molecular mechanisms of anther and its transcription regulations.Figure optionsDownload full-size imageDownload as PowerPoint slideResearch highlights► We extend the gene co-expression from pair identification to group mining. ► We perform co-expressed gene group mining based on maximum-clique graph algorithm. ► Total 254 Arabidopsis anther complete co-expression groups are obtained in large-scale analysis.

Keywords
Arabidopsis; Anther; Co-expression; Pathway; Maximum-clique algorithm
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 35, Issue 2, April 2011, Pages 62–68
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us