PubMed

Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome.

Rach EA, Yuan HY, Majoros WH, Tomancak P, Ohler U.

Genome Biol. 2009;10(7):R73. Epub 2009 Jul 9.PMID: 19589141 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational analysis of core promoters in the Drosophila genome.

Ohler U, Liao GC, Niemann H, Rubin GM.

Genome Biol. 2002;3(12):RESEARCH0087. Epub 2002 Dec 20.PMID: 12537576 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli.

Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juárez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E.

PLoS One. 2009 Oct 19;4(10):e7526.PMID: 19838305 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction.

Ohler U.

Nucleic Acids Res. 2006;34(20):5943-50. Epub 2006 Oct 26.PMID: 17068082 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters.

Ponjavic J, Lenhard B, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A.

Genome Biol. 2006;7(8):R78. Epub 2006 Aug 17.PMID: 16916456 [PubMed - indexed for MEDLINE]Related articlesFree article

Large-scale discovery of promoter motifs in Drosophila melanogaster.

Down TA, Bergman CM, Su J, Hubbard TJ.

PLoS Comput Biol. 2007 Jan 19;3(1):e7. Epub 2006 Dec 5.PMID: 17238282 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome wide analysis of Arabidopsis core promoters.

Molina C, Grotewold E.

BMC Genomics. 2005 Feb 25;6(1):25.PMID: 15733318 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparative promoter region analysis powered by CORG.

Dieterich C, Grossmann S, Tanzer A, Röpcke S, Arndt PF, Stadler PF, Vingron M.

BMC Genomics. 2005 Feb 21;6(1):24.PMID: 15723697 [PubMed - indexed for MEDLINE]Related articlesFree article

A transcription factor affinity-based code for mammalian transcription initiation.

Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG.

Genome Res. 2009 Apr;19(4):644-56. Epub 2009 Jan 13.PMID: 19141595 [PubMed - indexed for MEDLINE]Related articlesFree article

Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis.

Yamamoto YY, Yoshitsugu T, Sakurai T, Seki M, Shinozaki K, Obokata J.

Plant J. 2009 Oct;60(2):350-62. Epub 2009 Jun 29.PMID: 19563441 [PubMed - indexed for MEDLINE]Related articles

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.

Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE.

Genome Biol. 2004;5(9):R61. Epub 2004 Aug 20.PMID: 15345045 [PubMed - indexed for MEDLINE]Related articlesFree article

Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis.

Tanaka T, Koyanagi KO, Itoh T.

Plant Physiol. 2009 Mar;149(3):1316-24. Epub 2008 Dec 31.PMID: 19118127 [PubMed - indexed for MEDLINE]Related articlesFree article

V1R promoters are well conserved and exhibit common putative regulatory motifs.

Stewart R, Lane RP.

BMC Genomics. 2007 Jul 25;8:253.PMID: 17651493 [PubMed - indexed for MEDLINE]Related articlesFree article

Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster.

Zhu Q, Halfon MS.

BMC Genomics. 2009 Jan 7;10:9.PMID: 19128496 [PubMed - indexed for MEDLINE]Related articlesFree article

A comparative analysis of divergently-paired genes (DPGs) among Drosophila and vertebrate genomes.

Yang L, Yu J.

BMC Evol Biol. 2009 Mar 11;9:55.PMID: 19284596 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide analysis of mammalian promoter architecture and evolution.

Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engström PG, Frith MC, Forrest AR, Alkema WB, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K, Mottagui-Tabar S, Arner P, Chesi A, Gustincich S, Persichetti F, Suzuki H, Grimmond SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Y.

Nat Genet. 2006 Jun;38(6):626-35. Epub 2006 Apr 28. Erratum in: Nat Genet. 2007 Sep;39(9):1174. PMID: 16645617 [PubMed - indexed for MEDLINE]Related articles

Transcriptional features of genomic regulatory blocks.

Akalin A, Fredman D, Arner E, Dong X, Bryne JC, Suzuki H, Daub CO, Hayashizaki Y, Lenhard B.

Genome Biol. 2009;10(4):R38. Epub 2009 Apr 19.PMID: 19374772 [PubMed - indexed for MEDLINE]Related articlesFree article

Repetitive DNA elements, nucleosome binding and human gene expression.

Huda A, Mariño-Ramírez L, Landsman D, Jordan IK.

Gene. 2009 May 1;436(1-2):12-22. Epub 2009 Feb 5.PMID: 19393174 [PubMed - indexed for MEDLINE]Related articles

Functional conservation of Rel binding sites in drosophilid genomes.

Copley RR, Totrov M, Linnell J, Field S, Ragoussis J, Udalova IA.

Genome Res. 2007 Sep;17(9):1327-35.PMID: 17785540 [PubMed - indexed for MEDLINE]Related articlesFree article

Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters.

Yang C, Bolotin E, Jiang T, Sladek FM, Martinez E.

Gene. 2007 Mar 1;389(1):52-65. Epub 2006 Oct 10.PMID: 17123746 [PubMed - indexed for MEDLINE]Related articlesFree article