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Items: 1 to 20 of 90

1.

TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information.

Kulkarni SR, Vaneechoutte D, Van de Velde J, Vandepoele K.

Nucleic Acids Res. 2018 Apr 6;46(6):e31. doi: 10.1093/nar/gkx1279.

2.
3.

TF-finder: a software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base.

Cui X, Wang T, Chen HS, Busov V, Wei H.

BMC Bioinformatics. 2010 Aug 12;11:425. doi: 10.1186/1471-2105-11-425.

4.

TF-Cluster: a pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM).

Nie J, Stewart R, Zhang H, Thomson JA, Ruan F, Cui X, Wei H.

BMC Syst Biol. 2011 Apr 15;5:53. doi: 10.1186/1752-0509-5-53.

5.

Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis.

Darnell CL, Tonner PD, Gulli JG, Schmidler SC, Schmid AK.

mSystems. 2017 Sep 19;2(5). pii: e00032-17. doi: 10.1128/mSystems.00032-17. eCollection 2017 Sep-Oct.

6.

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.

7.

A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana.

Heyndrickx KS, Van de Velde J, Wang C, Weigel D, Vandepoele K.

Plant Cell. 2014 Oct;26(10):3894-910. doi: 10.1105/tpc.114.130591. Epub 2014 Oct 31.

8.

AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks.

Palaniswamy SK, James S, Sun H, Lamb RS, Davuluri RV, Grotewold E.

Plant Physiol. 2006 Mar;140(3):818-29.

9.

Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model.

Ingkasuwan P, Netrphan S, Prasitwattanaseree S, Tanticharoen M, Bhumiratana S, Meechai A, Chaijaruwanich J, Takahashi H, Cheevadhanarak S.

BMC Syst Biol. 2012 Aug 16;6:100. doi: 10.1186/1752-0509-6-100.

10.

A Machine Learning Approach to Predict Gene Regulatory Networks in Seed Development in Arabidopsis.

Ni Y, Aghamirzaie D, Elmarakeby H, Collakova E, Li S, Grene R, Heath LS.

Front Plant Sci. 2016 Dec 23;7:1936. doi: 10.3389/fpls.2016.01936. eCollection 2016.

11.

An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation.

Tian C, Zhang X, He J, Yu H, Wang Y, Shi B, Han Y, Wang G, Feng X, Zhang C, Wang J, Qi J, Yu R, Jiao Y.

Mol Syst Biol. 2014 Oct 30;10:755. doi: 10.15252/msb.20145470.

12.

Trimming of mammalian transcriptional networks using network component analysis.

Tran LM, Hyduke DR, Liao JC.

BMC Bioinformatics. 2010 Oct 13;11:511. doi: 10.1186/1471-2105-11-511.

13.

Inter- and intra-combinatorial regulation by transcription factors and microRNAs.

Zhou Y, Ferguson J, Chang JT, Kluger Y.

BMC Genomics. 2007 Oct 30;8:396.

14.

Synergistic regulatory networks mediated by microRNAs and transcription factors under drought, heat and salt stresses in Oryza Sativa spp.

Nigam D, Kumar S, Mishra DC, Rai A, Smita S, Saha A.

Gene. 2015 Jan 25;555(2):127-39. doi: 10.1016/j.gene.2014.10.054. Epub 2014 Oct 31.

PMID:
25445270
15.

Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant.

Defoort J, Van de Peer Y, Vermeirssen V.

Nucleic Acids Res. 2018 Jul 27;46(13):6480-6503. doi: 10.1093/nar/gky468.

16.

TOBFAC: the database of tobacco transcription factors.

Rushton PJ, Bokowiec MT, Laudeman TW, Brannock JF, Chen X, Timko MP.

BMC Bioinformatics. 2008 Jan 25;9:53. doi: 10.1186/1471-2105-9-53.

17.

Construction and analysis of microRNA-transcription factor regulation network in Arabidopsis.

Tang L, Zhang Z, Gu P, Chen M.

IET Syst Biol. 2014 Jun;8(3):76-86. doi: 10.1049/iet-syb.2013.0024.

PMID:
25014374
18.

AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana.

Chen YA, Wen YC, Chang WC.

BMC Genomics. 2012 Mar 8;13:85. doi: 10.1186/1471-2164-13-85.

19.

PlnTFDB: an integrative plant transcription factor database.

Riaño-Pachón DM, Ruzicic S, Dreyer I, Mueller-Roeber B.

BMC Bioinformatics. 2007 Feb 7;8:42.

20.

A genome-scale resource for the functional characterization of Arabidopsis transcription factors.

Pruneda-Paz JL, Breton G, Nagel DH, Kang SE, Bonaldi K, Doherty CJ, Ravelo S, Galli M, Ecker JR, Kay SA.

Cell Rep. 2014 Jul 24;8(2):622-32. doi: 10.1016/j.celrep.2014.06.033. Epub 2014 Jul 17.

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