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Items: 1 to 20 of 104

1.

FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces.

Contreras-Moreira B, Sebastian A.

Methods Mol Biol. 2016;1482:259-77. doi: 10.1007/978-1-4939-6396-6_17.

PMID:
27557773
2.

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces.

Sebastian A, Contreras-Moreira B.

Bioinformatics. 2014 Jan 15;30(2):258-65. doi: 10.1093/bioinformatics/btt663. Epub 2013 Nov 14.

PMID:
24234003
3.

Transcription factor-DNA binding: beyond binding site motifs.

Inukai S, Kock KH, Bulyk ML.

Curr Opin Genet Dev. 2017 Apr;43:110-119. doi: 10.1016/j.gde.2017.02.007. Epub 2017 Mar 27. Review.

4.

AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors.

Davuluri RV, Sun H, Palaniswamy SK, Matthews N, Molina C, Kurtz M, Grotewold E.

BMC Bioinformatics. 2003 Jun 23;4:25. Epub 2003 Jun 23.

5.

Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar.

Ding J, Hu H, Li X.

Plant Physiol. 2012 Jan;158(1):145-55. doi: 10.1104/pp.111.186080. Epub 2011 Nov 4.

6.

GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group.

Lee TY, Chang WC, Hsu JB, Chang TH, Shien DM.

BMC Genomics. 2012;13 Suppl 1:S3. doi: 10.1186/1471-2164-13-S1-S3. Epub 2012 Jan 17.

7.

In planta analysis of a cis-regulatory cytokinin response motif in Arabidopsis and identification of a novel enhancer sequence.

Ramireddy E, Brenner WG, Pfeifer A, Heyl A, Schmülling T.

Plant Cell Physiol. 2013 Jul;54(7):1079-92. doi: 10.1093/pcp/pct060. Epub 2013 Apr 24.

PMID:
23620480
8.

RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes.

Contreras-Moreira B, Castro-Mondragon JA, Rioualen C, Cantalapiedra CP, van Helden J.

Methods Mol Biol. 2016;1482:279-95. doi: 10.1007/978-1-4939-6396-6_18.

PMID:
27557774
9.

Quantitative statistical analysis of cis-regulatory sequences in ABA/VP1- and CBF/DREB1-regulated genes of Arabidopsis.

Suzuki M, Ketterling MG, McCarty DR.

Plant Physiol. 2005 Sep;139(1):437-47. Epub 2005 Aug 19.

10.

A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites.

Kulakovskiy IV, Belostotsky AA, Kasianov AS, Esipova NG, Medvedeva YA, Eliseeva IA, Makeev VJ.

Bioinformatics. 2011 Oct 1;27(19):2621-4. doi: 10.1093/bioinformatics/btr453. Epub 2011 Aug 18.

PMID:
21852305
11.

Biochemical and cellular characterization of transcription factors binding to the hyperconserved core promoter-associated M4 motif.

Trung NT, Kremmer E, Mittler G.

BMC Genomics. 2016 Aug 30;17:693. doi: 10.1186/s12864-016-3033-3.

12.

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.

13.

Evening expression of arabidopsis GIGANTEA is controlled by combinatorial interactions among evolutionarily conserved regulatory motifs.

Berns MC, Nordström K, Cremer F, Tóth R, Hartke M, Simon S, Klasen JR, Bürstel I, Coupland G.

Plant Cell. 2014 Oct;26(10):3999-4018. doi: 10.1105/tpc.114.129437. Epub 2014 Oct 31.

14.

COPS: detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets.

Ha N, Polychronidou M, Lohmann I.

PLoS One. 2012;7(12):e52055. doi: 10.1371/journal.pone.0052055. Epub 2012 Dec 18.

15.

Integration of bioinformatics and synthetic promoters leads to the discovery of novel elicitor-responsive cis-regulatory sequences in Arabidopsis.

Koschmann J, Machens F, Becker M, Niemeyer J, Schulze J, Bülow L, Stahl DJ, Hehl R.

Plant Physiol. 2012 Sep;160(1):178-91. doi: 10.1104/pp.112.198259. Epub 2012 Jun 28.

17.

PlantCARE, a plant cis-acting regulatory element database.

Rombauts S, Déhais P, Van Montagu M, Rouzé P.

Nucleic Acids Res. 1999 Jan 1;27(1):295-6.

18.

The in vivo dissection of direct RFX-target gene promoters in C. elegans reveals a novel cis-regulatory element, the C-box.

Burghoorn J, Piasecki BP, Crona F, Phirke P, Jeppsson KE, Swoboda P.

Dev Biol. 2012 Aug 15;368(2):415-26. doi: 10.1016/j.ydbio.2012.05.033. Epub 2012 Jun 5.

19.

Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription.

Berendzen KW, Weiste C, Wanke D, Kilian J, Harter K, Dröge-Laser W.

BMC Plant Biol. 2012 Aug 1;12:125. doi: 10.1186/1471-2229-12-125.

20.

Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs.

Starr MO, Ho MC, Gunther EJ, Tu YK, Shur AS, Goetz SE, Borok MJ, Kang V, Drewell RA.

Dev Biol. 2011 Nov 15;359(2):290-302. doi: 10.1016/j.ydbio.2011.07.028. Epub 2011 Jul 28.

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