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Items: 1 to 20 of 134

1.

Transcriptional coordination of the metabolic network in Arabidopsis.

Wei H, Persson S, Mehta T, Srinivasasainagendra V, Chen L, Page GP, Somerville C, Loraine A.

Plant Physiol. 2006 Oct;142(2):762-74. Epub 2006 Aug 18.

2.

Transcriptome coexpression analysis using ATTED-II for integrated transcriptomic/metabolomic analysis.

Yonekura-Sakakibara K, Saito K.

Methods Mol Biol. 2013;1011:317-26. doi: 10.1007/978-1-62703-414-2_25.

PMID:
23616007
3.

Large cliques in Arabidopsis gene coexpression network and motif discovery.

Zheng X, Liu T, Yang Z, Wang J.

J Plant Physiol. 2011 Apr 15;168(6):611-8. doi: 10.1016/j.jplph.2010.09.010. Epub 2010 Nov 1.

PMID:
21044807
4.

RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice.

Lee TH, Kim YK, Pham TT, Song SI, Kim JK, Kang KY, An G, Jung KH, Galbraith DW, Kim M, Yoon UH, Nahm BH.

Plant Physiol. 2009 Sep;151(1):16-33. doi: 10.1104/pp.109.139030. Epub 2009 Jul 15.

5.

Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks.

Vandepoele K, Quimbaya M, Casneuf T, De Veylder L, Van de Peer Y.

Plant Physiol. 2009 Jun;150(2):535-46. doi: 10.1104/pp.109.136028. Epub 2009 Apr 8.

6.

The transcript and metabolite networks affected by the two clades of Arabidopsis glucosinolate biosynthesis regulators.

Malitsky S, Blum E, Less H, Venger I, Elbaz M, Morin S, Eshed Y, Aharoni A.

Plant Physiol. 2008 Dec;148(4):2021-49. doi: 10.1104/pp.108.124784. Epub 2008 Oct 1.

7.

Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes.

Wada M, Takahashi H, Altaf-Ul-Amin M, Nakamura K, Hirai MY, Ohta D, Kanaya S.

Gene. 2012 Jul 15;503(1):56-64. doi: 10.1016/j.gene.2012.04.043. Epub 2012 Apr 24.

8.

Coexpression of neighboring genes in the genome of Arabidopsis thaliana.

Williams EJ, Bowles DJ.

Genome Res. 2004 Jun;14(6):1060-7.

9.

Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics.

Naika M, Shameer K, Sowdhamini R.

Mol Biosyst. 2013 Jul;9(7):1888-908. doi: 10.1039/c3mb70072k. Epub 2013 May 3.

PMID:
23645342
10.

CressExpress: a tool for large-scale mining of expression data from Arabidopsis.

Srinivasasainagendra V, Page GP, Mehta T, Coulibaly I, Loraine AE.

Plant Physiol. 2008 Jul;147(3):1004-16. doi: 10.1104/pp.107.115535. Epub 2008 May 8.

11.

ATTED-II provides coexpressed gene networks for Arabidopsis.

Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K.

Nucleic Acids Res. 2009 Jan;37(Database issue):D987-91. doi: 10.1093/nar/gkn807. Epub 2008 Oct 25.

13.

Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm.

Mutwil M, Usadel B, Schütte M, Loraine A, Ebenhöh O, Persson S.

Plant Physiol. 2010 Jan;152(1):29-43. doi: 10.1104/pp.109.145318. Epub 2009 Nov 4.

14.

MetaCyc and AraCyc. Metabolic pathway databases for plant research.

Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp PD, Rhee SY.

Plant Physiol. 2005 May;138(1):27-37.

15.

The TAIR database.

Poole RL.

Methods Mol Biol. 2007;406:179-212.

PMID:
18287693
16.

PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis.

Pan D, Sun N, Cheung KH, Guan Z, Ma L, Holford M, Deng X, Zhao H.

BMC Bioinformatics. 2003 Nov 7;4:56.

17.

Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana.

Kusano M, Fukushima A, Arita M, Jonsson P, Moritz T, Kobayashi M, Hayashi N, Tohge T, Saito K.

BMC Syst Biol. 2007 Nov 21;1:53.

18.

A transcriptional dynamic network during Arabidopsis thaliana pollen development.

Wang J, Qiu X, Li Y, Deng Y, Shi T.

BMC Syst Biol. 2011;5 Suppl 3:S8. doi: 10.1186/1752-0509-5-S3-S8. Epub 2011 Dec 23.

19.
20.

Genome-wide analysis of hydrogen peroxide-regulated gene expression in Arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis.

Vanderauwera S, Zimmermann P, Rombauts S, Vandenabeele S, Langebartels C, Gruissem W, Inzé D, Van Breusegem F.

Plant Physiol. 2005 Oct;139(2):806-21. Epub 2005 Sep 23.

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