Advanced Genomic Data Mining

PLoS Computational Biology

Volumn 4, Issue 9, 2008, Pages

  Fernández Suárez, Xosé M ^a   Birney, Ewan ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DATA;

DATA MINING;

EID: 84869228154     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000121     Document Type: Article

References (34)

1. Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, et al.(2004) An overview of Ensembl. Genome Research 14: 925-928.
2. Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, et al.(2007) Ensembl 2007. Nucleic Acids Res 35: D610-D617.
3. Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, et al.(2007) The UCSC Genome Browser database: Update 2007. Nucleic Acids Res 35: D668-D673.
4. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, et al.(2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res 32: D 493-D496.
5. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, et al.(2005) Galaxy: A platform for interactive large-scale genome analysis. Genome Research 15: 1451-1455.
6. de la Cruz N, Bromberg S, Pasko D, Shimoyama M, Twigger S, et al.(2005) The rat genome database (RGD): Developments towards a phenome database. Nucleic Acids Research 33: D485-D491.
7. Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ, et al.(2007) The Rat Genome Database, update 2007-Easing the path from disease to data and back again. Nucleic Acids Res 35: D658-D662.
8. Chen N, Harris TW, Antoshechkin I, Bastiani C, Bieri T, et al.(2005) WormBase: A comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res 33: D383-D389.
9. Harris TW, Stein LD, (2006) WormBase: Methods for data mining and comparative genomics. In: Strange K, editors. Methods in Molecular Biology in C. elegans: Methods and Applications 351 New Jersey Humana Press pp. 31-50.
10. Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, et al.(2004) EnsMart: A generic system for fast and flexible access to biological data. Genome Research 14: 160-169.
11. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al.(2004) BioConductor: Open software development for computational biology and bioinformatics. Genome Biology 5: R80.
12. Gentleman RC, Carey V, Hüber W, Irizarry R, Dudoit R, eds. (2005) Bioinformatics and Computational Biology Solutions Using R and BioConductor Springer.
13. Vastrik I, D'Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, et al.(2007) Reactome: A knowledge base of biologic pathways and processes. Genome Biology 8: R39.
14. UniProt Consortium(2007) The Universal Protein Resource (UniProt). Nucleic Acids Res 35: D193-D197.
15. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al.(2000) Gene Ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 25: 25-29.
16. Ihaka R, Gentleman R, (1996) R: A language for data analysis and graphics. Journal of Computational and Graphical Statistics 5: 299-314.
17. Becker RA, Chambers JM, Wilks AR, (1988) The New S Language: A Programming Environment for Data Analysis and Graphics Pacific Grove (California) Wadsworth & Brooks/Cole.
18. Ashurst JL, Chen CK, Gilbert JG, Jekosch K, Keenan S, et al.(2005) The vertebrate genome annotation (VEGA) database. Nucleic Acids Res 33: D459-D465.
19. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, et al.(2001) dbSNP: The NCBI database of genetic variation. Nucleic Acids Res 29: 308-311.
20. Jaiswal P, Ni J, Yap I, Ware D, Spooner W, et al.(2006) Gramene: A bird's eye view of cereal genomes. Nucleic Acids Res 34: D717-D723.
21. Pruitt KD, Tatusova T, Maglott DR, (2007) NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35: D61-D65.
22. Maglott D, Ostell J, Pruitt KD, Tatusova T, (2007) Entrez gene: Gene-centered information at NCBI. Nucleic Acids Res 35: D26-D31.
23. Eisen MB, Spellman PT, Brown PO, Botstein D, (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863-14868.
24. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, et al.(1999) Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286: 531-537.
25. Segal E, Friedman N, Kaminski N, Regev A, Koller D, (2005) From signatures to models: Understanding cancer using microarrays. Nature Genetics 37: S38-S45.
26. Diez D, Alvarez R, Dopazo A, (2007) Codelink: An R package for analysis of GE healthcare gene expression bioarrays. Bioinformatics 23: 1168-1169.
27. Davidson LA, Nguyen DV, Hokanson RM, Callaway ES, Isett RB, et al.(2004) Chemopreventive n-3 polyunsaturated fatty acids reprogram genetic signatures during colon cancer initiation and progression in the rat. Cancer Res 64: 6797-6804.
28. Ramakrishnan R, Dorris D, Lublinsky A, Nguyen A, Domanus M, et al.(2002) An assessment of Motorola CodeLink microarray performance for gene expression profiling applications. Nucleic Acids Res 30: e30.
29. Taylor J, Schenk I, Blankenberg D, Nekrutenko A, (2007) Using Galaxy to Perform Large-Scale Interactive Data Analysis. Current Protocols in Bioinformatics 10.5.1 (Supplement 19).
30. Rice P, Longden I, Bleasby A, (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 16: 276-277.
31. Pratap J, Javed A, Languino LR, van Wijnen AJ, Stein JL, et al.(2005) The Runx2 osteogenic transcription factor regulates matrix metalloproteinase 9 in bone metastatic cancer cells and controls cell invasion. Molecular and Cellular Biology 25: 8581-8591.
32. Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, et al.(2006) Taverna: A tool for building and running workflows of services. Nucleic Acids Res 34: W729-W732.
33. Alonso G, Casati F, Kuno H, Machiraju V, (2004) Web Services: Concepts, Architectures and Applications. Data-Centric Systems and Applications Berlin/Heidelberg Springer-Verlag.
34. Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L, (2001) The distributed annotation system. BMC Bioinformatics 2: 7.