Curated databases and their role in clinical bioinformatics

 

• References

• 1 Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H. et al. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 1991; 252: 1651-6.
• 2 Lee Y, Sultana R, Pertea G , Cho J, Karamycheva S, Tsai J. et al. Crossreferencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Res 2002; 12: 493-502.
• 3 Flores-Morales A, Stahlberg N. Tollet-Egnell P, Lundeberg J , Malek RL, Quackenbush J. et al. Microarray analysis of the in vivo effects of hypophysectomy and growth hormone treatment on gene expression in the rat. Endocrinology 2001; 142: 3163-76.
• 4 Rudd S. Expressed sequence tags: alternative or complement to whole genome sequences?. Trends Plant Sci 2003; 8: 321-9.
• 5 Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995; 269: 496-512.
• 6 Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H. et al. Life with 6000 genes. Science 1996; 274 546 563-67.
• 7 The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 1998; 282: 2012-8.
• 8 Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG. et al. The genome sequence of Drosophila melanogaster. Science 2000; 287: 2185-95.
• 9 Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J. et al. Initial sequencing and analysis of the human genome. Nature 2001; 409: 860-921.
• 10 Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG. et al. The sequence of the human genome. Science 2001; 291: 1304-51.
• 11 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002; 420: 520-62.
• 12 Collins FS, Morgan M, Patrinos A. The Human Genome Project: lessons from large-scale biology. Science 2003; 300: 286-90.
• 13 Green ED. Strategies for the systematic sequencing of complex genomes. Nat Rev Genet 2001; 2: 573-83.
• 14 Goffeau A, Aert R, Agostini-Carbone ML, Ahmed A, Aigle M, Alberghina L. et al. The yeast genome directory. Nature 1997; 387 Suppl 5-6.
• 15 Waterston RH, Lander ES, Sulston JE. On the sequencing of the human genome. Proc Natl Acad Sci U.S.A 2002; 99: 3712-6.
• 16 Waterston RH, Lander ES, Sulston JE. More on the sequencing of the human genome. Proc Natl Acad Sci U.S.A 2003; 100: 3022-4.
• 17 Eddy SR. Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2001; 2: 919-29.
• 18 Reik W, Walter J. Genomic imprinting: parental influence on the genome. Nat Rev Genet 2001; 2: 21-32.
• 19 Mattick JS, Gagen MJ. The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol Biol Evol 2002; 18: 1611-30.
• 20 Nomura N, Miyajima N, Sazuka T, Tanaka A, Kawarabayasi Y, Sato S. et al. Prediction of the coding sequences of unidentified human genes. I. The coding sequences of 40 new genes (KIAA0001-KIAA0040) deduced by analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1 (supplement). DNA Res 1994; 1: 47-56.
• 21 Strausberg RL, Feingold EA, Klausner RD, Collins FS. The mammalian gene collection. Science 1999; 286: 455-7.
• 22 Wiemann S, Weil B, Wellenreuther R, Gassenhuber J, Glassl S, Ansorge W. et al. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. Genome Res 2001; 11: 422-35.
• 23 Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002; 420: 563-73.
• 24 Cyranoski D. Geneticists lay foundations for human transcriptome database. Nature 2002; 419: 3-4.
• 25 Quackenbush J. The power of public access: the human genome project and the scientific process. Nat Genet 2001; 29: 4-6.
• 26 Katsanis N, Worley KC, Lupski JR. An evaluation of the draft human genome sequence. Nat Genet 2001; 29: 88-91.
• 27 Olson MV, Varki A. Sequencing the chimpanzee genome: insights into human evolution and disease. Nat Rev Genet 2003; 4: 20-8.
• 28 Zhang MQ. Computational prediction of eukaryotic protein-coding genes. Nat Rev Genet 2002; 3: 698-709.
• 29 Mathe C, Sagot MF, Schiex T, Rouze P. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res 2002; 30: 4103-17.
• 30 Reese MG, Kulp D, Tammana H, Haussler D. Genie—gene finding in Drosophila melanogaster. Genome Res 2000; 10: 529-38.
• 31 Guigo R, Agarwal P, Abril JF, Burset M, Fickett JW. An assessment of gene prediction accuracy in large DNA sequences. Genome Res 2000; 10: 1631-42.
• 32 Wolfsberg TG, Landsman D. A comparison of expressed sequence tags (ESTs) to human genomic sequences. Nucleic Acids Res 1997; 25: 1626-32.
• 33 Ureta-Vidal A, Ettwiller L, Birney E. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat Rev Genet 2003; 4: 251-62.
• 34 Osada N, Hida M, Kusuda J, Tanuma R, Iseki K, Hirata M. et al. Assignment of 118 novel cDNAs of cynomolgus monkey brain to human chromosomes. Gene 2001; 275: 31-7.
• 35 Pennacchio LA, Rubin EM. Comparative genomic tools and databases: providing insights into the human genome. J Clin Invest 2003; 111: 1099-106.
• 36 Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT. et al. The UCSC Genome Browser Database. Nucleic Acids Res 2003; 31: 51-4.
• 37 Wheeler DL, Church DM, Federhen S , Lash AE, Madden TL, Pontius JU. et al. Database resources of the National Center for Biotechnology. Nucleic Acids Res 2003; 31: 28-33.
• 38 Clamp M, Andrews D, Barker D, Bevan P, Cameron G, Chen Y. et al. Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res 2003; 31: 38-42.
• 39 Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA. et al. VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 2000; 16: 1046-7.
• 40 Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J. et al. PipMaker - a web server for aligning two genomic DNA sequences. Genome Res 2000; 10: 577-86.
• 41 Ma MK, Woo MH, McLeod HL. Genetic basis of drug metabolism. Am J Health Syst Pharm 2002; 59: 2061-9.
• 42 Pirmohamed M, Park BK. Genetic susceptibility to adverse drug reactions. Trends Pharmacol Sci 2001; 22: 298-305.
• 43 Halapi E, Hakonarson H. Advances in the development of genetic markers for the diagnosis of disease and drug response. Expert Rev Mol Diagn 2002; 2: 411-21.
• 44 Immervoll T, Wjst M. Current status of the Asthma and Allergy Database. Nucleic Acids Res 1999; 27: 213-4.
• 45 Melton L. Pharmacogenetics and genotyping: on the trail of SNPs. Nature 2003; 422 917 923.-46.
• 46 Risch N, Merikangas K. The future of genetic studies of complex human diseases. Science 2001; 273: 1516-7.
• 47 Carlson CS, Eberle MA, Rieder MJ, Smith JD, Kruglyak L, Nickerson DA. Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat Genet 2003; 33: 518-21.
• 48 Cardon LR, Abecasis GR. Using haplotype blocks to map human complex trait loci. Trends Genet 2003; 19: 135-40.
• 49 Couzin J. Human genome. HapMap launched with pledges of $100 million. Science 2002; 298: 941-2.
• 50 Kota R, Rudd S, Facius A, Kolesov G, Thiel T, Zhang H. et al. Snipping polymorphisms from large EST collection in barley (Hordeum vulgare L.). Journal of Molecular Genetics and Genomics. In press. 2003
• 51 Stefansson SE, Jonsson H, Ingvarsson T, Manolescu I, Jonsson HH, Olafsdottir G. et al. Genomewide scan for hand osteoarthritis: a novel mutation in matrilin-3. Am J Hum Genet 2003; 72: 1448-59.
• 52 Modrek B, Lee C. A genomic view of alternative splicing. Nat Genet 2002; 30: 13-9.
• 53 Zavolan M, Kondo S, Schonbach C, Adachi J, Hume DA, Hayashizaki Y. et al. Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res 2003; 13: 1290-300.
• 54 Fairbrother WG, Yeh RF, Sharp PA, Burge CB. Predictive identification of exonic splicing enhancers in human genes. Science 2002; 297: 1007-13.
• 55 Yeakley JM, Fan JB, Doucet D, Luo L, Wickham E, Ye Z. et al. Profiling alternative splicing on fiber-optic arrays. Nat Biotechnol 2002; 20: 353-8.
• 56 Claes K, Poppe B, Machackova E, Coene I, Foretova L, De Paepe A. et al. Differentiating pathogenic mutations from polymorphic alterations in the splice sites of BRCA1 and BRCA2. Genes Chromosomes Cancer 2003; 37: 314-20.
• 57 Tsunoda T, Inada H, Kalembeyi I, Imanaka-Yoshida K, Sakakibara M, Okada R. et al. Involvement of large tenascin-C splice variants in breast cancer progression. Am J Pathol 2003; 162: 1857-67.
• 58 Smith TL, Pearson ML, Wilcox KR, Cruz C, Lancaster MV, Robinson-Dunn B. et al. Emergence of vancomycin resistance in Staphylococcus aureus. Glycopeptide- Intermediate Staphylococcus aureus Working Group. N Engl J Med 1999; 340: 493-501.
• 59 Tomasini ML, Zanussi S, Sozzi M, Tedeschi R, Basaglia G, De Paoli P. Heterogeneity of cag genotypes in Helicobacter pylori isolates from human biopsy specimens. J Clin Microbiol 2003; 41: 976-80.
• 60 Woolhouse ME, Webster JP, Domingo E, Charlesworth B, Levin BR. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat Genet 2002; 32: 569-77.
• 61 Pizza M, Scarlato V, Masignani V, Giuliani MM, Arico B, Comanducci M. et al. Identification of vaccine candidates against serogroup B meningococcus by wholegenome sequencing. Science 2000; 287: 1816-20.
• 62 Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD. et al. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 2003; 299: 2071-4.
• 63 Buchrieser C, Rusniok C, Kunst F, Cossart P, Glaser P. Comparison of the genome sequences of Listeria monocytogenes and Listeria innocua: clues for evolution and pathogenicity. FEMS Immunol Med Microbiol 2003; 35: 207-13.
• 64 Perna NT, Plunkett III G, Burland V, Mau B, Glasner JD, Rose DJ. et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 2001; 409: 529-33.
• 65 Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V. et al. Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 2003; 423: 87-91.
• 66 Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE. et al. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 2003; 423: 81-6.
• 67 Read TD, Salzberg SL, Pop M, Shumway M, Umayam L, Jiang L. et al. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 2002; 296: 2028-33.
• 68 Cole ST, Barrell BG. Analysis of the genome of Mycobacterium tuberculosis H37Rv. Novartis Found Symp 1998; 217: 160-72.
• 69 Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR. et al. Massive gene decay in the leprosy bacillus. Nature 2001; 409: 1007-11.
• 70 Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J. et al. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol 2002; 184: 5479-90.
• 71 Garnier T, Eiglmeier K, Camus JC, Medina N, Mansoor H, Pryor M. et al. The complete genome sequence of Myco - bacterium bovis. Proc Natl Acad Sci U.S.A 2003; 100: 7877-82.
• 72 Alm RA, Ling LS, Moir DT, King BL, Brown ED, Doig PC. et al. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 1999; 397: 176-80.
• 73 Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci U.S.A 2000; 97: 14668-73.
• 74 Balfe P, Simmonds P, Ludlam CA, Bishop JO, Brown AJ. Concurrent evolution of human immunodeficiency virus type 1 in patients infected from the same source: rate of sequence change and low frequency of inactivating mutations. J Virol 1990; 64: 6221-33.
• 75 Yoshimura FK, Diem K. Learn Jr. GH, Riddell S, Corey L. Intrapatient sequence variation of the gag gene of human immunodeficiency virus type 1 plasma virions. J Virol 1996; 70: 8879-87.
• 76 Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR. et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science 2002; 298: 129-49.
• 77 Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW. et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002; 419: 498-511.
• 78 Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC. et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 2002; 419: 512-9.
• 79 Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR. et al. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 2002; 298: 149-59.
• 80 Ranson H, Claudianos C, Ortelli F, Abgrall C, Hemingway J, Sharakhova MV. et al. Evolution of supergene families associated with insecticide resistance. Science 2002; 298: 179-81.
• 81 Wu CH, Yamaguchi Y, Benjamin LR, Horvat-Gordon M, Washinsky J, Enerly E. et al. NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. Genes Dev 2003; 17: 1402-14.
• 82 Gu CC, Rao DC, Stormo G, Hicks C, Province MA. Role of gene expression microarray analysis in finding complex disease genes. Genet Epidemiol 2002; 23: 37-56.
• 83 Slonim DK. From patterns to pathways: gene expression data analysis comes of age. Nat Genet 2002; 32 Suppl 502-8.
• 84 Valafar F. Pattern recognition techniques in microarray data analysis: a survey. Ann N.Y. Acad Sci 2002; 980: 41-64.
• 85 Glynne RJ, Watson SR. The immune system and gene expression microarrays— new answers to old questions. J Pathol 2001; 195: 20-30.
• 86 Granucci F, Vizzardelli C, Virzi E, Rescigno M, Ricciardi-Castagnoli P. Transcriptional reprogramming of dendritic cells by differentiation stimuli. Eur J Immunol 2001; 31: 2539-46.
• 87 Schmidt-Weber CB, Wohlfahrt JG, Blaser K. DNA arrays in allergy and immunology. Int Arch Allergy Immunol 2001; 126: 1-10.
• 88 Nau GJ, Richmond JF, Schlesinger A, Jennings EG, Lander ES, Young RA. Human macrophage activation programs induced by bacterial pathogens. Proc Natl Acad Sci U.S.A 2002; 99: 1503-8.
• 89 Zhang Y, Luxon BA, Casola A, Garofalo RP, Jamaluddin M, Brasier AR. Expression of respiratory syncytial virus-induced chemokine gene networks in lower airway epithelial cells revealed by cDNA microarrays. J Virol 2001; 75: 9044-58.
• 90 Ehrt S, Schnappinger D, Bekiranov S, Drenkow J, Shi S, Gingeras TR. et al. Reprogramming of the macrophage transcriptome in response to interferongamma and Mycobacterium tuberculosis: signaling roles of nitric oxide synthase-2 and phagocyte oxidase. J Exp Med 2001; 194: 1123-40.
• 91 Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M. et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002; 415: 530-6.
• 92 Ringner M, Peterson C, Khan J. Analyzing array data using supervised methods. Pharmacogenomics 2002; 3: 403-15.
• 93 Fayyad UP-SGS. From Data Mining to Knowledge Discovery in Databases. AI Magazine Fall. 1996: 37-54.
• 94 Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C. et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001; 29: 365-71.
• 95 Frishman D, Mokrejs M , Kosykh D, Kastenmuller G, Kolesov G, Zubrzycki I. et al. The PEDANT genome database. Nucleic Acids Res 2003; 31: 207-11.
• 96 Gene Ontology Consortium. Creating the gene ontology resource: design and implementation. Genome Res 2001; 11: 1425-33.
• 97 Stoesser G, Baker W, van den BA. Garcia-Pastor M, Kanz C, Kulikova T. et al. The EMBL Nucleotide Sequence Database: major new developments. Nucleic Acids Res 2003; 31: 17-22.
• 98 Wilkinson MD, Links M. (2002) Bio MOBY: an open source biological web services proposal. Brief Bioinform 2002; 3: 331-41.
• 99 Miyazaki S, Sugawara H, Gojobori T, Tateno Y. DNA Data Bank of Japan (DDBJ) in XML. Nucleic Acids Res 2003; 31: 13-6.
• 100 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL. Gen Bank. Nucleic Acids Res 2002; 30: 17-20.
• 101 Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A. et al. The Inter Pro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 2003; 31: 315-8.
• 102 Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res 2003; 31: 371-3.
• 103 Wu CH, Yeh LS, Huang H, Arminski L, Castro-Alvear J , Chen Y. et al. The Protein Information Resource. Nucleic Acids Res 2003; 31: 345-7.
• 104 Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E. et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2033. Nucleic Acids Res 2003; 31: 365-70.
• 105 FlyBase Consortium. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res 2003; 31: 172-5.
• 106 Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M. et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res 2002; 30: 31-4.
• 107 Blake JA, Richardson JE, Bult CJ, Kadin JA, Eppig JT. (2003) MGD: the Mouse Genome Database. Nucleic Acids Res 2003; 31: 193-5.
• 108 Twigger S, Lu J, Shimoyama M, Chen D, Pasko D, Long H. et al. Rat Genome Database (RGD): mapping disease onto the genome. Nucleic Acids Res 2002; 30: 125-8.
• 109 Harris TW, Lee R, Schwarz E, Bradnam K, Lawson D, Chen W. et al. Worm Base: a cross-species database for comparative genomics. Nucleic Acids Res 2003; 31: 133-7.
• 110 Peterson JD, Umayam LA, Dickinson T, Hickey EK, White O. The Comprehensive Microbial Resource. Nucleic Acids Res 2001; 29: 123-5.
• 111 Perriere G, Duret L, Gouy M. HOBACGEN: database system for comparative genomics in bacteria. Genome Res 2000; 10: 379-85.
• 112 Bahl A, Brunk B, Crabtree J, Fraunholz MJ, Gajria B, Grant GR. et al. Plasmo DB: the Plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Res 2003; 31: 212-5.
• 113 Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS. et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 2001; 29: 22-8.
• 114 Dieterich C, Wang H , Rateitschak K, Luz H, Vingron M. CORG: a database for COmparative Regulatory Genomics. Nucleic Acids Res 2003; 31: 55-7.
• 115 Glasner JD, Liss P, Plunkett III G, Darling A, Prasad T, Rusch M. et al. ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res 2003; 31: 147-51.
• 116 Dralyuk I, Brudno M, Gelfand MS, Zorn M, Dubchak I. ASDB: database of alternatively spliced genes. Nucleic Acids Res 2000; 28: 296-7.
• 117 Pospisil H, Herrmann A, Pankow H, Reich JG. A database on alternative splice forms on the Integrated Genetic Map Service (IGMS). In Silico. Biol 2002; 3: 20.
• 118 Modrek B, Resch A, Grasso C, Lee C. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res 2001; 29: 2850-9.
• 119 Fredman D, Siegfried M, Yuan YP, Bork P, Lehvaslaiho H, Brookes AJ. HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources. Nucleic Acids Res 2002; 30: 387-91.
• 120 Hirakawa M, Tanaka T, Hashimoto Y, Kuroda M, Takagi T, Nakamura Y. JSNP: a database of common gene variations in the Japanese population. Nucleic Acids Res 2002; 30: 158-62.
• 121 Huang HD, Horng JT, Lee CC, Liu BJ. ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data. Genome Biol 2003; 4-R29.
• 122 Burset M, Seledtsov IA, Solovyev VV. Splice DB: database of canonical and noncanonical mammalian splice sites. Nucleic Acids Res 2001; 29: 255-9.
• 123 Krause A, Haas S.A, Coward E, Vingron M. (2002) SYSTERS, Gene Nest, Splice Nest: exploring sequence space from genome to protein. Nucleic Acids Res., 30. 2002: 299-300.
• 124 Thorisson GA, Stein LD. The SNP Consortium website: past, present and future. Nucleic Acids Res 2003; 31: 124-7.
• 125 Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N. et al. Array Express—a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003; 31: 68-71.
• 126 Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002; 30: 207-10.
• 127 Bono H, Kasukawa T, Hayashizaki Y, Okazaki Y. READ: RIKEN Expression Array Database. Nucleic Acids Res 2002; 30: 211-3.
• 128 Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM. et al. The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res 2003; 31: 94-6.
• 129 Karp PD, Riley M, Saier M, Paulsen IT, Paley SM, Pellegrini-Toole A. The Eco Cyc and MetaCyc databases. Nucleic Acids Res 2000; 28: 56-9.
• 130 Kanehisa M, Goto S, Kawashima S, Nakaya A. The KEGG databases at Genome Net. Nucleic Acids Res 2002; 30: 42-6.
• 131 Salgado H, Santos-Zavaleta A. Gama-Castro S, Millan-Zarate D, Diaz-Peredo E, Sanchez-Solano F. et al. Regulon DB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K- 12. Nucleic Acids Res 2001; 29: 72-4.
• 132 Safran M, Solomon I, Shmueli O, Lapidot M, Shen-Orr S, Adato A. et al. Gene Cards 2002: towards a complete, object-oriented, human gene compendium. Bioinformatics 2002; 18: 1542-3.
• 133 Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence project: update and current status. Nucleic Acids Res 2003; 31: 34-7.