Literature DB >> 20305269

CoP: a database for characterizing co-expressed gene modules with biological information in plants.

Yoshiyuki Ogata1, Hideyuki Suzuki, Nozomu Sakurai, Daisuke Shibata.   

Abstract

UNLABELLED: Using a large dataset (10 022 assays) obtained from public plant microarray databases, we developed the CoP database for associating co-expressed gene modules with biological information such as gene ontology terms and, if available, metabolic pathway names. The Confeito algorithm developed previously in our laboratory, which is suitable to calculate the interconnectivity between genes in co-expressed gene network, was applied to extract co-expressed gene modules. The database includes the gene modules for Arabidopsis thaliana (thale cress) and seven crops, Glycine max (soybean), Hordeum vulgare (barley), Oryza sativa (rice), Populus trichocarpa (poplar), Triticum aestivum (wheat), Vitis vinifera (grape) and Zea mays (maize). AVAILABILITY: The CoP database is available at: http://webs2.kazusa.or.jp/kagiana/cop0911/.

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Mesh：

Year:  2010        PMID： 20305269     DOI： 10.1093/bioinformatics/btq121

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  40 in total

Review 1.  Transcriptional and metabolic programs following exposure of plants to UV-B irradiation.

Authors:  Takayuki Tohge; Miyako Kusano; Atsushi Fukushima; Kazuki Saito; Alisdair R Fernie
Journal:  Plant Signal Behav       Date:  2011-12

2.  Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches.

Authors:  Atsushi Fukushima; Tomoko Nishizawa; Mariko Hayakumo; Shoko Hikosaka; Kazuki Saito; Eiji Goto; Miyako Kusano
Journal:  Plant Physiol       Date:  2012-02-03       Impact factor: 8.340

3.  PlaNet: combined sequence and expression comparisons across plant networks derived from seven species.

Authors:  Marek Mutwil; Sebastian Klie; Takayuki Tohge; Federico M Giorgi; Olivia Wilkins; Malcolm M Campbell; Alisdair R Fernie; Björn Usadel; Zoran Nikoloski; Staffan Persson
Journal:  Plant Cell       Date:  2011-03-25       Impact factor: 11.277

4.  Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice.

Authors:  Stephen P Ficklin; F Alex Feltus
Journal:  Plant Physiol       Date:  2011-05-23       Impact factor: 8.340

5.  Strategies to explore functional genomics data sets in NCBI's GEO database.

Authors:  Stephen E Wilhite; Tanya Barrett
Journal:  Methods Mol Biol       Date:  2012

6.  The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks.

Authors:  Stephen P Ficklin; Feng Luo; F Alex Feltus
Journal:  Plant Physiol       Date:  2010-07-28       Impact factor: 8.340

Review 7.  Engineering crassulacean acid metabolism to improve water-use efficiency.

Authors:  Anne M Borland; James Hartwell; David J Weston; Karen A Schlauch; Timothy J Tschaplinski; Gerald A Tuskan; Xiaohan Yang; John C Cushman
Journal:  Trends Plant Sci       Date:  2014-02-19       Impact factor: 18.313

8.  Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data.

Authors:  Ji Huang; Stefania Vendramin; Lizhen Shi; Karen M McGinnis
Journal:  Plant Physiol       Date:  2017-08-02       Impact factor: 8.340

9.  Understanding the Molecular Drivers of Disease Heterogeneity in Crohn's Disease Using Multi-omic Data Integration and Network Analysis.

Authors:  Padhmanand Sudhakar; Bram Verstockt; Jonathan Cremer; Sare Verstockt; João Sabino; Marc Ferrante; Séverine Vermeire
Journal:  Inflamm Bowel Dis       Date:  2021-05-17       Impact factor: 5.325

10.  Discriminative local subspaces in gene expression data for effective gene function prediction.

Authors:  Tomas Puelma; Rodrigo A Gutiérrez; Alvaro Soto
Journal:  Bioinformatics       Date:  2012-07-20       Impact factor: 6.937
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