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Literature DB >> 12671007

GALA, a database for genomic sequence alignments and annotations.

Belinda Giardine¹, Laura Elnitski, Cathy Riemer, Izabela Makalowska, Scott Schwartz, Webb Miller, Ross C Hardison.

Abstract

We have developed a relational database to contain whole genome sequence alignments between human and mouse with extensive annotations of the human sequence. Complex queries are supported on recorded features, both directly and on proximity among them. Searches can reveal a wide variety of relationships, such as finding all genes expressed in a designated tissue that have a highly conserved noncoding sequence 5' to the start site. Other examples are finding single nucleotide polymorphisms that occur in conserved noncoding regions upstream of genes and identifying CpG islands that overlap the 5' ends of divergently transcribed genes. The database is available online at http://globin.cse.psu.edu/ and http://bio.cse.psu.edu/.

Entities: Gene Species

Mesh：

Substances：
5' Untranslated Regions

Year: 2003 PMID： 12671007 PMCID： PMC430176 DOI： 10.1101/gr.603103

Source DB: PubMed Journal: Genome Res ISSN： 1088-9051 Impact factor: 9.043

32 in total

1. 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

2. dbSNP: the NCBI database of genetic variation.

Authors: S T Sherry; M H Ward; M Kholodov; J Baker; L Phan; E M Smigielski; K Sirotkin
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

3. RefSeq and LocusLink: NCBI gene-centered resources.

Authors: K D Pruitt; D R Maglott
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

4. 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

5. Integrating genomic homology into gene structure prediction.

Authors: I Korf; P Flicek; D Duan; M R Brent
Journal: Bioinformatics Date: 2001 Impact factor: 6.937

6. Conserved noncoding sequences are reliable guides to regulatory elements.

Authors: R C Hardison
Journal: Trends Genet Date: 2000-09 Impact factor: 11.639

7. Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5.

Authors: M D Wilson; C Riemer; D W Martindale; P Schnupf; A P Boright; T L Cheung; D M Hardy; S Schwartz; S W Scherer; L C Tsui; W Miller; B F Koop
Journal: Nucleic Acids Res Date: 2001-03-15 Impact factor: 16.971

Review 8. Genomic strategies to identify mammalian regulatory sequences.

Authors: L A Pennacchio; E M Rubin
Journal: Nat Rev Genet Date: 2001-02 Impact factor: 53.242

9. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons.

Authors: G G Loots; R M Locksley; C M Blankespoor; Z E Wang; W Miller; E M Rubin; K A Frazer
Journal: Science Date: 2000-04-07 Impact factor: 47.728

10. Comparative sequence analysis of the mouse and human Lgn1/SMA interval.

Authors: M Endrizzi; S Huang; J M Scharf; A R Kelter; B Wirth; L M Kunkel; W Miller; W F Dietrich
Journal: Genomics Date: 1999-09-01 Impact factor: 5.736

21 in total

1. Identification and characterization of multi-species conserved sequences.

Authors: Elliott H Margulies; Mathieu Blanchette; David Haussler; Eric D Green
Journal: Genome Res Date: 2003-12 Impact factor: 9.043

2. Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies.

Authors: George P Patrinos; Belinda Giardine; Cathy Riemer; Webb Miller; David H K Chui; Nicholas P Anagnou; Henri Wajcman; Ross C Hardison
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

3. EnsMart: a generic system for fast and flexible access to biological data.

Authors: Arek Kasprzyk; Damian Keefe; Damian Smedley; Darin London; William Spooner; Craig Melsopp; Martin Hammond; Philippe Rocca-Serra; Tony Cox; Ewan Birney
Journal: Genome Res Date: 2004-01 Impact factor: 9.043

4. ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.

Authors: Ivan Ovcharenko; Marcelo A Nobrega; Gabriela G Loots; Lisa Stubbs
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

5. Exploring relationships and mining data with the UCSC Gene Sorter.

Authors: W J Kent; Fan Hsu; Donna Karolchik; Robert M Kuhn; Hiram Clawson; Heather Trumbower; David Haussler
Journal: Genome Res Date: 2005-05 Impact factor: 9.043

6. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression.

Authors: Mathieu Blanchette; Alain R Bataille; Xiaoyu Chen; Christian Poitras; Josée Laganière; Céline Lefèbvre; Geneviève Deblois; Vincent Giguère; Vincent Ferretti; Dominique Bergeron; Benoit Coulombe; François Robert
Journal: Genome Res Date: 2006-04-10 Impact factor: 9.043