Statistical Viewer: A tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Stenger, Judith E ^a   Xu, Hong ^a   Haynes, Carol ^a   Hauser, Elizabeth R ^a   Pericak Vance, Margaret ^a   Goldschmidt Clermont, Pascal J ^a   Vance, Jeffery M ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANNOTATION SYSTEMS; ASSOCIATION ANALYSIS; BIOLOGICAL DATABASE; DISEASE SUSCEPTIBILITY GENES; FEATURE ANNOTATION; GENOME ANNOTATION; REGIONS OF INTEREST; STATISTICAL DATAS;

DATA VISUALIZATION; STATISTICS; TOOLS;

GENES;

ARTICLE; COMPUTER PROGRAM; COMPUTER SYSTEM; DISEASE PREDISPOSITION; GENE EXPRESSION; GENE LOCATION; GENE MAPPING; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC LINKAGE; GENOME ANALYSIS; HUMAN; HUMAN GENOME; MARKER GENE; STATISTICAL ANALYSIS; BIOLOGY; CHROMOSOME MAP; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER LANGUAGE; CONTIG MAPPING; DATA BASE; FACTUAL DATABASE; GENETIC DATABASE; GENOME; GENOMICS; INFORMATION RETRIEVAL; PROCEDURES; STATISTICAL MODEL;

CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; CONTIG MAPPING; DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; DATABASES, GENETIC; GENETIC LINKAGE; GENOME; GENOME, HUMAN; GENOMICS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; MODELS, STATISTICAL; PROGRAMMING LANGUAGES; SOFTWARE; SOFTWARE DESIGN; USER-COMPUTER INTERFACE;

EID: 25444465138     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-95     Document Type: Article

References (37)

1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Geneontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
2. Stein LD: Integrating biological databases. Nat Rev Genet 2003, 4:337-345.
3. Hubbard T: Biological information: making it accessible and integrated (and trying to make sense of it). Bioinformatics 2002, 18(Suppl 2):S140.
4. Heumann K, Harris C, Mewes HW: A top-down approach to whole genome visualization. Proc Int Conf Intell Syst Mol Biol 1996, 4:98-108.
5. Tatusova TA, Karsch-Mizrachi I, Ostell JA: Complete genomes in WWW Entrez: data representation and analysis. Bioinformatics 1999, 15:536-543.
6. NCBI Map Viewer [http://www.ncbi.nlm.nih.gov/mapview/]
7. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M: The Ensembl genome database project. Nucleic Acids Res 2002, 30:38-41.
8. Project Ensembl Genome Browser [http://www.ensembl.org.]
9. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. Genome Res 2002, 12:996-1006.
10. UCSC Genome Bioinformatics [http://genome.cse.ucsc.edu/]
11. Hauser MA, Li YJ, Takeuchi S, Walters R, Noureddine M, Maready M, Darden T, Hulette C, Martin E, Hauser E, Xu H, Schmechel D, Stenger JE, Dietrich F, Vance J: Genomic convergence: identifying candidate genes for Parkinson's disease by combining serial analysis of gene expression and genetic linkage. Hum Mol Genet 2003, 12:671-677.
12. Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G, Shlien A, Palsson ST, Frigge ML, Thorgeirsson TE, Gulcher JR, Stefansson K: A high-resolution recombination map of the human genome. Nat Genet 2002, 31:241-247.
13. UniSTS integrated makers and maps [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists]
14. Schuler GD: Pieces of the puzzle: expressed sequence tags and the catalog of human genes. J Mol Med 1997, 75:694-698.
15. Olson M, Hood L, Cantor C, Botstein D: A common language for physical mapping of the human genome. Science 1989, 245:1434-5.
16. NCBI UniSTS ftp site [ftp://ftp.ncbi.nlm.nih.gov/repository/UniSTS/]
17. Schuler GD: Sequence mapping by electronic PCR. Genome Res 1997, 7:541-50.
18. Rotmistrovsky K, Jang W, Schuler GD: A web server for performing electronic PCR. Nucleic Acids Res 2004:W108-12.
19. NCBI e-PCR [http://www.ncbi.nlm.nih.gov/genome/sts/epcr.cgi]
20. Kent WJ: BLAT - the BLAST-like alignment tool. Genome Res 2002, 12:656-664.
21. Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L: The distributed annotation system. BMC Bioinformatics 2001, 2:7.
22. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E: The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12:1611-1618.
23. McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, Gregory SG, Humphray SJ, French L, Evans RS, Bethel G, Whittaker A, Holden JL, McCann OT, Dunham A, Soderlund C, Scott CE, Bentley DR, Schuler G, Chen HC, Jang W, Green ED, Idol JR, Maduro VV, Montgomery KT, Lee E, Miller A, Emerling S, Kucherlapati, Gibbs R, Scherer S, Gorrell JH, Sodergren E, Clerc-Blankenburg K, Tabor P, Naylor S, Garcia D, De Jong PJ, Catanese JJ, Nowak N, Osoegawa K, Qin S, Rowen L, Madan A, Dors M, Hood L, Trask B, Friedman C, Massa H, Cheung VG, Kirsch IR, Reid T, Yonescu R, Weissenbach J, Bruls T, Heilig R, Branscomb E, Olsen A, Doggett N, Cheng JF, Hawkins T, Myers RM, Shang J, Ramirez L, Schmutz J, Velasquez O, Dixon K, Stone NE, Cox DR, Haussler D, Kent WJ, Furey T, Rogic S, Kennedy S, Jones S, Rosenthal A, Wen G, Schilhabel M, Gloeckner G, Nyakatura G, Siebert R, Schlegelberger B, Korenberg J, Chen XN, Fujiyama A, Hattori M, Toyoda A, Yada T, Park HS, Sakaki Y, Shimizu N, et al: A physical map of the human genome. Nature 2001, 409:934-941.
24. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di FV, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, et al: The sequence of the human genome. Science 2001, 291:1304-1351.
25. Lander ES, Green P: Construction of multi-locus genetic linkage maps in humans. Proc Natl Acad Sci USA 1987, 84:2363-2367.
26. Marshfield Medical Center Genetics [http://research.marshfieldclinic.org/genetics/]
27. Dib C, Faure S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S, Hazan J, Seboun E, Lathrop M, Gyapay G, Morissette J, Weissenbach J: A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 1996, 380:152-4.
28. Galperin MY: The molecular biology database collection: 2005 update. Nucleic Acids Res 2005:D5-24.
29. Li YJ, Oliveira SA, Xu P, Martin ER, Stenger JE, Hulette C, Scherzer CR, Hauser MA, Scott WK, Small GW, Nance MA, Watts RL, Hubble JP, Koller WC, Pahwa R, Stern MB, Hiner BC, Jankovic J, Goetz CG, Mastaglia F, Middleton LT, Roses AD, Saunders AM, Welsh-Bohmer KA, Schmechel DE, Gullans SR, Haines JL, Gilbert JR, Vance JM, Pericak-Vance MA: Glutathione S-transferase omega-1 modifies age-at-onset of Alzheimer disease and Parkinson disease. Hum Mol Genet 2004, 13:573.
30. Lobachev KS, Stenger JE, Kozyreva OG, Jurka J, Gordenin DA, Resnick MA: Inverted Alu repeats unstable in yeast are excluded from the human genome. EMBO J 2000, 19:3822-3830.
31. Stenger JE, Lobachev KS, Gordenin D, Darden TA, Jurka J, Resnick MA: Biased distribution of inverted and direct Alus in the human genome: implications for insertion, exclusion, and genome stability. Genome Res 2001, 11:12-27.
32. Duke Center for Human Genetics Software Repository [http://wwwchg.duhs.duke.edu/software/index.html]
33. Download Ensembl Wiki web URL [http://www.ensembl.org/Docs/wiki/html/EnsemblDocs/DownloadEnsembl.html]
34. Ensembl Anonymous FTP site [ftp://ftp.ensembl.org/pub/]
35. Ensembl installation instructions pdf file [http://www.ensembl.org/Docs/linked_docs/EnsemblInstall_29.pdf]
36. GZIP [http://www.gzip.org/]
37. WinZip Windows Archive Utility [http://www.winzip.com/]