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Literature DB >> 12409480

EZ-Retrieve: a web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites.

Haibo Zhang¹, Y Ramanathan, Patricia Soteropoulos, Michael L Recce, Peter P Tolias.

Abstract

The availability of a draft human genome sequence and ability to monitor the transcription of thousands of genes with DNA microarrays has necessitated the need for new computational tools that can analyze cis-regulatory elements controlling genes that display similar expression patterns. We have developed a tool designated EZ-Retrieve that can: (i) retrieve any particular region of human genome sequence from the NCBI database and (ii) analyze retrieved sequences for putative transcription factor-binding sites (TFBSs) as they appear on the TRANSFAC database. The tool is web-based, user-friendly and offers both batch sequence retrieval and batch TFBS prediction. A major application of EZ-Retrieve is the analysis of co-expressed genes that are highlighted as expression clusters in DNA microarray experiments.

Entities: Gene Species

Mesh：

Substances：

Year: 2002 PMID： 12409480 PMCID： PMC135846 DOI： 10.1093/nar/gnf120

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

17 in total

1. Assessing clusters and motifs from gene expression data.

Authors: L M Jakt; L Cao; K S Cheah; D K Smith
Journal: Genome Res Date: 2001-01 Impact factor: 9.043

2. E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis.

Authors: H Müller; A P Bracken; R Vernell; M C Moroni; F Christians; E Grassilli; E Prosperini; E Vigo; J D Oliner; K Helin
Journal: Genes Dev Date: 2001-02-01 Impact factor: 11.361

3. The TRANSFAC system on gene expression regulation.

Authors: E Wingender; X Chen; E Fricke; R Geffers; R Hehl; I Liebich; M Krull; V Matys; H Michael; R Ohnhäuser; M Prüss; F Schacherer; S Thiele; S Urbach
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

4. Regulatory element detection using correlation with expression.

Authors: H J Bussemaker; H Li; E D Siggia
Journal: Nat Genet Date: 2001-02 Impact factor: 38.330

5. 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

6. PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches.

Authors: W Fujibuchi; J S Anderson; D Landsman
Journal: Nucleic Acids Res Date: 2001-10-01 Impact factor: 16.971

Review 7. Core promoters: active contributors to combinatorial gene regulation.

Authors: S T Smale
Journal: Genes Dev Date: 2001-10-01 Impact factor: 11.361

8. Identifying regulatory networks by combinatorial analysis of promoter elements.

Authors: Y Pilpel; P Sudarsanam; G M Church
Journal: Nat Genet Date: 2001-10 Impact factor: 38.330

Review 9. The E2F transcription factors: key regulators of cell proliferation.

Authors: H Müller; K Helin
Journal: Biochim Biophys Acta Date: 2000-02-14

Review 10. Large-scale gene expression data analysis: a new challenge to computational biologists.

Authors: M Q Zhang
Journal: Genome Res Date: 1999-08 Impact factor: 9.043

11 in total

1. FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes.

Authors: Allen Chong; Guanglan Zhang; Vladimir B Bajic
Journal: Nucleic Acids Res Date: 2003-07-01 Impact factor: 16.971

2. 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

3. BEARR: Batch Extraction and Analysis of cis-Regulatory Regions.

Authors: Vinsensius B Vega; Dhinoth Kumar Bangarusamy; Lance D Miller; Edison T Liu; Chin-Yo Lin
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

4. Reliable prediction of transcription factor binding sites by phylogenetic verification.

Authors: Xiaoman Li; Sheng Zhong; Wing H Wong
Journal: Proc Natl Acad Sci U S A Date: 2005-11-14 Impact factor: 11.205

5. Expression profiling of human hepatoma cells reveals global repression of genes involved in cell proliferation, growth, and apoptosis upon infection with parvovirus H-1.

Authors: Jianhong Li; Ekkehard Werner; Manfred Hergenhahn; Rémy Poirey; Zuyu Luo; Jean Rommelaere; Jean-Claude Jauniaux
Journal: J Virol Date: 2005-02 Impact factor: 5.103

6. ALU repeats in promoters are position-dependent co-response elements (coRE) that enhance or repress transcription by dimeric and monomeric progesterone receptors.

Authors: Britta M Jacobsen; Purevsuren Jambal; Stephanie A Schittone; Kathryn B Horwitz
Journal: Mol Endocrinol Date: 2009-04-16