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Gene coexpression network analysis as a source of functional annotation for rice genes.

Childs KL, Davidson RM, Buell CR.

PLoS One. 2011;6(7):e22196. doi: 10.1371/journal.pone.0022196. Epub 2011 Jul 22.


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

Ficklin SP, Luo F, Feltus FA.

Plant Physiol. 2010 Sep;154(1):13-24. doi: 10.1104/pp.110.159459. Epub 2010 Jul 28.


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

Fukushima A, Nishizawa T, Hayakumo M, Hikosaka S, Saito K, Goto E, Kusano M.

Plant Physiol. 2012 Apr;158(4):1487-502. doi: 10.1104/pp.111.188367. Epub 2012 Feb 3.


Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops.

Mochida K, Uehara-Yamaguchi Y, Yoshida T, Sakurai T, Shinozaki K.

Plant Cell Physiol. 2011 May;52(5):785-803. doi: 10.1093/pcp/pcr035. Epub 2011 Mar 24.


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

Ficklin SP, Feltus FA.

Plant Physiol. 2011 Jul;156(3):1244-56. doi: 10.1104/pp.111.173047. Epub 2011 May 23.


Systematic identification of functional plant modules through the integration of complementary data sources.

Heyndrickx KS, Vandepoele K.

Plant Physiol. 2012 Jul;159(3):884-901. doi: 10.1104/pp.112.196725. Epub 2012 May 15. Erratum in: Plant Physiol. 2012 aUG;159(4):1875.


RiceFREND: a platform for retrieving coexpressed gene networks in rice.

Sato Y, Namiki N, Takehisa H, Kamatsuki K, Minami H, Ikawa H, Ohyanagi H, Sugimoto K, Itoh J, Antonio BA, Nagamura Y.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1214-21. doi: 10.1093/nar/gks1122. Epub 2012 Nov 24.


Characterization of WRKY co-regulatory networks in rice and Arabidopsis.

Berri S, Abbruscato P, Faivre-Rampant O, Brasileiro AC, Fumasoni I, Satoh K, Kikuchi S, Mizzi L, Morandini P, Pè ME, Piffanelli P.

BMC Plant Biol. 2009 Sep 22;9:120. doi: 10.1186/1471-2229-9-120.


ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.

Obayashi T, Nishida K, Kasahara K, Kinoshita K.

Plant Cell Physiol. 2011 Feb;52(2):213-9. doi: 10.1093/pcp/pcq203. Epub 2011 Jan 7.


Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules.

Okamura Y, Obayashi T, Kinoshita K.

PLoS One. 2015 Jul 6;10(7):e0132039. doi: 10.1371/journal.pone.0132039. eCollection 2015.


Identification of rice genes associated with cosmic-ray response via co-expression gene network analysis.

Hwang SG, Kim DS, Hwang JE, Han AR, Jang CS.

Gene. 2014 May 15;541(2):82-91. doi: 10.1016/j.gene.2014.02.060. Epub 2014 Mar 12.


Genomic survey, expression profile and co-expression network analysis of OsWD40 family in rice.

Ouyang Y, Huang X, Lu Z, Yao J.

BMC Genomics. 2012 Mar 20;13:100. doi: 10.1186/1471-2164-13-100.


Module Based Differential Coexpression Analysis Method for Type 2 Diabetes.

Yuan L, Zheng CH, Xia JF, Huang DS.

Biomed Res Int. 2015;2015:836929. doi: 10.1155/2015/836929. Epub 2015 Aug 3.


DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules.

Tesson BM, Breitling R, Jansen RC.

BMC Bioinformatics. 2010 Oct 6;11:497. doi: 10.1186/1471-2105-11-497.


PlantExpress: A Database Integrating OryzaExpress and ArthaExpress for Single-species and Cross-species Gene Expression Network Analyses with Microarray-Based Transcriptome Data.

Kudo T, Terashima S, Takaki Y, Tomita K, Saito M, Kanno M, Yokoyama K, Yano K.

Plant Cell Physiol. 2017 Jan 1;58(1):e1. doi: 10.1093/pcp/pcw208.


Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles.

Prieto C, Risueño A, Fontanillo C, De las Rivas J.

PLoS One. 2008;3(12):e3911. doi: 10.1371/journal.pone.0003911. Epub 2008 Dec 15.


A developmental transcriptional network for maize defines coexpression modules.

Downs GS, Bi YM, Colasanti J, Wu W, Chen X, Zhu T, Rothstein SJ, Lukens LN.

Plant Physiol. 2013 Apr;161(4):1830-43. doi: 10.1104/pp.112.213231. Epub 2013 Feb 6.


Comprehensive network analysis of anther-expressed genes in rice by the combination of 33 laser microdissection and 143 spatiotemporal microarrays.

Aya K, Suzuki G, Suwabe K, Hobo T, Takahashi H, Shiono K, Yano K, Tsutsumi N, Nakazono M, Nagamura Y, Matsuoka M, Watanabe M.

PLoS One. 2011;6(10):e26162. doi: 10.1371/journal.pone.0026162. Epub 2011 Oct 26.


Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules.

Filichkin SA, Breton G, Priest HD, Dharmawardhana P, Jaiswal P, Fox SE, Michael TP, Chory J, Kay SA, Mockler TC.

PLoS One. 2011;6(6):e16907. doi: 10.1371/journal.pone.0016907. Epub 2011 Jun 9.


Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing.

Watanabe KA, Homayouni A, Tufano T, Lopez J, Ringler P, Rushton P, Shen QJ.

DNA Res. 2015 Oct;22(5):319-29. doi: 10.1093/dnares/dsv015. Epub 2015 Sep 3.

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