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Literature DB >> 12824364

PromoSer: A large-scale mammalian promoter and transcription start site identification service.

Anason S Halees¹, Dmitriy Leyfer, Zhiping Weng.

Abstract

Proximal promoters have a major impact on transcriptional regulation. Studies of the sequence-based nature of this regulation usually require collection of proximal promoter sequences for large sets of co-regulated genes. We report a newly implemented web service that facilitates extraction of user specified regions around the transcription start site of all annotated human, mouse or rat genes. The transcription start sites have been identified computationally by considering alignments of a large number of partial and full-length mRNA sequences to genomic DNA, with provision for alternative promoters. The service is publicly available at http://biowulf.bu.edu/zlab/PromoSer/.

Entities: Species

Mesh：

Substances：
RNA, Messenger

Year: 2003 PMID： 12824364 PMCID： PMC168956 DOI： 10.1093/nar/gkg549

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

37 in total

1. Creation of genome-wide protein expression libraries using random activation of gene expression.

Authors: J J Harrington; B Sherf; S Rundlett; P D Jackson; R Perry; S Cain; C Leventhal; M Thornton; R Ramachandran; J Whittington; L Lerner; D Costanzo; K McElligott; S Boozer; R Mays; E Smith; N Veloso; A Klika; J Hess; K Cothren; K Lo; J Offenbacher; J Danzig; M Ducar
Journal: Nat Biotechnol Date: 2001-05 Impact factor: 54.908

2. Identification and analysis of eukaryotic promoters: recent computational approaches.

Authors: U Ohler; H Niemann
Journal: Trends Genet Date: 2001-02 Impact factor: 11.639

3. Initial sequencing and analysis of the human genome.

Authors: E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal: Nature Date: 2001-02-15 Impact factor: 49.962

4. First pass annotation of promoters on human chromosome 22.

Authors: M Scherf; A Klingenhoff; K Frech; K Quandt; R Schneider; K Grote; M Frisch; V Gailus-Durner; A Seidel; R Brack-Werner; T Werner
Journal: Genome Res Date: 2001-03 Impact factor: 9.043

Review 5. Full-length cDNAs: more than just reaching the ends.

Authors: M Das; I Harvey; L L Chu; M Sinha; J Pelletier
Journal: Physiol Genomics Date: 2001-07-17 Impact factor: 3.107

6. Promoter prediction in the human genome.

Authors: S Hannenhalli; S Levy
Journal: Bioinformatics Date: 2001 Impact factor: 6.937

7. Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles.

Authors: D Y Chiang; P O Brown; M B Eisen
Journal: Bioinformatics Date: 2001 Impact factor: 6.937

8. Systematic variation in gene expression patterns in human cancer cell lines.

Authors: D T Ross; U Scherf; M B Eisen; C M Perou; C Rees; P Spellman; V Iyer; S S Jeffrey; M Van de Rijn; M Waltham; A Pergamenschikov; J C Lee; D Lashkari; D Shalon; T G Myers; J N Weinstein; D Botstein; P O Brown
Journal: Nat Genet Date: 2000-03 Impact factor: 38.330

Review 9. Going the distance: a current view of enhancer action.

Authors: E M Blackwood; J T Kadonaga
Journal: Science Date: 1998-07-03 Impact factor: 47.728

10. Cluster analysis and display of genome-wide expression patterns.

Authors: M B Eisen; P T Spellman; P O Brown; D Botstein
Journal: Proc Natl Acad Sci U S A Date: 1998-12-08 Impact factor: 11.205

33 in total

1. PromoSer: improvements to the algorithm, visualization and accessibility.

Authors: Anason S Halees; Zhiping Weng
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

2. SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation.

Authors: Zhenjun Hu; Yutao Fu; Anason S Halees; Szymon M Kielbasa; Zhiping Weng
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

3. MotifViz: an analysis and visualization tool for motif discovery.

Authors: Yutao Fu; Martin C Frith; Peter M Haverty; Zhiping Weng
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

4. Rapid identification of novel functional promoters for gene therapy.

Authors: Ian A Pringle; Deborah R Gill; Mary M Connolly; Anna E Lawton; Anne-Marie Hewitt; Graciela Nunez-Alonso; Seng H Cheng; Ronald K Scheule; Lee A Davies; Stephen C Hyde
Journal: J Mol Med (Berl) Date: 2012-07-06 Impact factor: 4.599

5. Green fluorescent protein reporter system with transcriptional sequence heterogeneity for monitoring the interferon response.

Authors: Linah Mahmoud; Maher Al-Saif; Haitham M Amer; Mustafa Sheikh; Fahad N Almajhdi; Khalid S A Khabar
Journal: J Virol Date: 2011-07-13 Impact factor: 5.103

6. Molecular determinants of crosstalk between nuclear receptors and toll-like receptors.

Authors: Sumito Ogawa; Jean Lozach; Chris Benner; Gabriel Pascual; Rajendra K Tangirala; Stefan Westin; Alexander Hoffmann; Shankar Subramaniam; Michael David; Michael G Rosenfeld; Christopher K Glass
Journal: Cell Date: 2005-09-09 Impact factor: 41.582