Functional genomics: Going forwards from the databases

Current Opinion in Genetics and Development

Volumn 7, Issue 6, 1997, Pages 777-783

  Rastan, Sohaila ^a   Beeley, Lee J ^a  

^a GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

DATA BASE; GENE FUNCTION; GENE SEQUENCE; GENOME; INFORMATION SERVICE; PRIORITY JOURNAL; REVIEW;

EID: 0031459311     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(97)80040-8     Document Type: Article

References (68)

1. Zhang Y, Proenca R, Maffei M, Barone M, Leopold L, Friedman JM. Positional cloning of the mouse obese gene and its human homologue [published erratum appears in Nature 1995 30:374(6521):479 [see comments]. Nature. 372:1994;425-432.
2. Tavtigian SV, Simard J, Rommens J, Couch F, Shattuck Eidens D, Neuhausen S, Merajver S, Thorlacius S, Offit K, Stoppa Lyonne D, et al. The complete BRCA2 gene and mutations in chromosome 13q-linked kindreds [see comments]. Nat Genet. 12:1996;333-337.
3. Chandrasekharappa SC, Guru SC, Manickam P, Olufemi SE, Collins FS, Emmert Buck MR, Debelenko LV, Zhuang Z, Lubensky LA, Liotta LA, et al. Positional cloning of the gene for multiple endocrine neoplasia-type 1. Science. 276:1997;404-407.
4. Heppner C, Kester MB, Agarwal SK, Debelenko LV, Emmert Buck MR, Guru SC, Manickam P, Olufemi SE, Skarulis MC, Doppman JL, et al. Somatic mutation of the MEN1 gene in parathyroid tumours. Nat Genet. 16:1997;375-378.
5. Mewes HW, Albermann K, Bahr M, Frishman D, Gleissner A, Hani J, Heumann K, Kleine K, Maierl A, Oliver SG, et al. Overview of the yeast genome. Nature. 387:1997;7-65.
6. Waterston RH, Sulston JE, Coulson AR. The Genome. Riddle DL, Blumenthal T, Meyer BJ, Priess JR. C. elegans II. 1997;23-45 CSHL Press, Cold Spring Harbor, NY.
7. Karp PD. Database links are a foundation for interoperability. Trends Biotechnol. 14:1996;273-279.
8. Beeley, LJ, Smith, RAG, Arch, JRS, Structural predictions for Leptin': a lesson in conserved structure and function 3rd International Symposium Obesity and NIDDM, Buckingham, UK, July 1996.
9. Madej T, Boguski MS, Bryant SH. Threading analysis suggests that the obese gene product may be a helical cytokine. FEBS Lett. 373:1995;13-18.
10. Beeley LJ, Smith RAG: Patent WO9638586: Method for detecting compounds that mimic, potentiate or inhibit the effect of the ob-protein. 1997.
11. Fickett JW. Finding genes by computer: the state of the art. Trends Genet. 12:1996;316-320.
12. Uberbacher EC, Xu Y, Mural RJ. Discovering and understanding genes in human DNA sequence using GRAIL. Doolittle RF. Methods in Enzymology. 1996;259-281 Academic Press, San Diego.
13. Gish W, States DJ. Identification of protein coding regions by database similarity search. Nat Genet. 3:1993;266-272.
14. Claverie JM. Effective large-scale sequence similarity searches. Methods Enzymol. 266:1996;212-227.
15. Rawlings CJ, Searls DB. Computational gene discovery and human disease. of special interest Curr Opin Genet Dev. 7:1997;416-423 The role of bioinformatics in expediting our understanding of human genetics is reviewed, with a focus on unravelling gene function using the electronic tools that are becoming available to all scientists.
16. Drake FH, Dodds RA, James LE, Connor JR, Debouck C, Richardson S, Lee Rykaczewski E, Coleman L, Rieman D, Barthlow R, et al. Cathepsin K, but not cathepsins B, L, or S, is abundantly expressed in human osteoclasts. J Biol Chem. 271:1996;12511-12516.
17. Zhao B, Janson CA, Amegadzie BY, D'Alessio K, Griffin C, Hanning CR, Jones C, Kurdyla J, McQueney M, Qiu X, et al. Crystal structure of human cathespin K complex with E-64. Nat Struct Biol. 4:1997;109-111.
18. McGrath ME, Klaus JL, Barnes MG, Bromme D. Crystal structure of human cathespin K complexed with a potent inhibitor. Nat Struct Biol. 4:1997;105-109.
19. Henikoff JG, Henikoff S. Blocks database and its applications. Methods Enzymol. 266:1996;88-105.
20. Bairoch A, Bucher P, Hofmann K. The PROSITE database, its status in 1997. Nucleic Acids Res. 25:1997;217-221.
21. Attwood TK, Beck ME, Bleasby AJ, Degtyarenko K, Michie AD, Parry Smith DJ. Novel developments with the PRINTS protein fingerprint database. Nucleic Acids Res. 25:1997;212-217.
22. Eddy SR. Hidden Markov models. Curr Opin Struct Biol. 6:1996;361-365.
23. Pedersen AG, Baldi P, Brunak S, Chauvin Y. Characterization of prokaryotic and eukaryotic promoters using hidden Markov models. Ismb. 4:1996;182-191.
24. Kulp D, Haussler D, Reese MG, Eeckman FH. A generalized hidden Markov model for the recognition of human genes in DNA. Isbm. 4:1996;134-142.
25. Sonnhammer EL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins. 28:1997;405-420.
26. Rost B. TOPITS: threading one-dimensional predictions into three-dimensional structures. Ismb. 3:1995;314-321.
27. Henikoff S, Greene EA, Pietrokovski S, Bark P, Attwood TK, Hood L. Gene families: the taxonomy of protein paralogs and chimeras. Science. 278:1997;609.
28. Bassett DR Jr, Boguski MS, Hieter P. Yeast genes and human disease [letter]. Nature. 379:1996;589-590.
29. Leach FS, Nicolaides NC, Papadopoulos N, Liu B, Jen J, Parsons R, Peltomaki P, Sistonen P, Aaltonen LA, Nystrom Lahti M, et al. Mutations of a mutS homolog in hereditary nonpolyposis colorectal cancer. Cell. 75:1993;1215-1225.
30. Sargent CA, Affara NA, Bentley E, Pelmear A, Bailey DM, Davey P, Dow D, Leversha M, Aplin H, Besley GT, et al. Cloning of the X-linked glycerol kinase deficiency gene and its identification by sequence comparison to the Bacillus subtilis homologue [see comments]. Hum Mol Genet. 2:1993;97-106.
31. Sun ZS, Albrecht U, Zhuchenko O, Bailey J, Eichele G, Lee CC. RIGUI, a putative mammalian ortholog of the Drosophila period gene. of special interest Cell. 90:1997;1003-1011 This work exemplifies the power of using Drosophila phenotypes in the search for mammalian genes that are responsible for fundamental control mechanisms. In this example, the putative mammalian orthologue of the Drosophila period gene was identified, which is a potential molecular component of a mammalian circadian clock mechanism.
32. Tugendreich S, Boguski MS, Seldin MS, Hieter P. Linking yeast genetics to mammalian genomes: identification and mapping of the human homolog of CDC27 via the expressed sequence tag (EST) data base. Proc Natl Acad Sci USA. 90:1993;10031-10035.
33. Banfi S, Borsani G, Rossi E, Bernard L, Guffanti A, Rubboli F, Marchitiello A, Giglio S, Coluccia E, Zollo M, et al. Identification and mapping of human cDNAs homologous to Drosophila mutant genes through EST database searching [see comments]. of special interest Nat Genet. 13:1996;167-174 This work stands as an excellent example of the use of model organism databases to probe human sequence data. It takes advantage of homology data of human ESTs to known Drosophila genes and the well-defined phenotypes arising from mutations in these genes to identify novel human genes and their potential function.
34. Gelbart WM, Crosby M, Matthews B, Rindone WP, Chillemi J, Russo Twombly S, Emmert D, Ashburner M, Drysdale RA, Whitfield E, et al. FlyBase: a Drosophila database. The FlyBase consortium. Nucleic Acids Res. 25:1997;63-66.
35. Zou H, Henzel Wj, Liu X, Lutschg A, Wang X. Apaf-1, a human protein homologous to C. elegans CED-4, participates in cytochrome c dependent activation of caspase-3. Cell. 90:1997;405-413.
36. Hengartner MO, Horvitz HR. Programmed cell death in Caenorhabditis elegans. Curr Opin Genet Dev. 4:1994;581-586.
37. Kalchman MA, Koide HB, Mccutcheon K, Graham RK, Nichol K, Nishiyama K, Kazemi Esfarjani P, Lynn FC, Wellington C, Metzler M, et al. HIP1, a human homologue of S. cerevisiae Sla2p, interacts with membrane-associated huntingtin in the brain. Nat Genet. 16:1997;44-53.
38. Latif F, Duh FM, Bader S, Sekido Y, Li H, Geil L, Zbar B, Minna JD, Lerman MI. The human homolog of the rodent immediate early response genes, PC4 and TIS7, resides in the lung cancer tumor suppressor gene region on chromosome 3p21. Hum Genet. 99:1997;334-341.
39. Bassett DE Jr, Boguski MS, Spencer F, Reeves R, Kim S, Weaver T, Hieter P. Genome cross-referencing and XREFdb: implications for the identification and analysis of genes mutated in human disease. of outstanding interest Nat Genet. 15:1997;339-344 The authors describe a project that is systematically identifying novel EST sequences that are highly related to genes in model organisms and mapping them to positions on the mouse and human maps. This process effectively cross-references model organism genes with mapped mammalian phenotypes, facilitating the identification of genes mutated in human disease states via the positional candidate approach.
40. Oliver SG. From DNA sequence to biological function [see comments]. Nature. 379:1996;597-600.
41. Ahringer J. Turn to the worm. Curr Opin Genet Dev. 7:1997;410-415.
42. Various authors Zebrafish Issue. Development. 1996;123.
43. Kornfeld K. Vulval development in Caenorhabditis elegans. of outstanding interest Trends Genet. 13:1997;55-61 A review of recent experiments that have begun to characterise molecules that mediate patterns of cell divisions and cell fates in C. elegans and explore the relationships between different signalling pathways. It exemplifies the power of genetic suppressor and enhancer analysis in this organism in dissecting biological pathways. Many of these molecules and signalling pathways have been conserved during evolution, suggesting that mechanisms used to establish patterns of cell fates have also been conserved.
44. Kornfeld K, Guan KL, Horvitz HR. The Caenorhabditis elegans gene mek-2 is required for vulval induction and encodes a protein similar to the protein kinase MEK. Genes Dev. 9:1995;756-768.
45. Wu Y, Han M, Guan KL. MEK-2, a Caenorhabditis elegans MAP kinase kinase, functions in Ras-mediated vulval induction and other developmental events. Genes Dev. 9:1995;742-755.
46. Forrester LM, Nagy A, Sam M, Watt A, Stevenson L, Bernstein A, Joyner AL, Wurst W. An induction gene trap screen in embryonic stem cells: Identification of genes that respond to retinoic acid in vitro. Proc Natl Acad Sci USA. 93:1996;1677-1682.
47. Friedrich G, Soriano P. Promoter traps in embryonic stem cells: a genetic screen to identify and mutate developmental genes in mice. Genes Dev. 5:1991;1513-1523.
48. Gossler A, Joyner AL, Rossant J, Skarnes WC. Mouse embryonic stem cells and reporter constructs to detect developmentally regulated genes. Science. 244:1989;463-465.
49. Scherer CA, Chen J, Nachabeh A, Hopkins N, Ruley HE. Transcriptional specificity of the pluripotent embryonic stem cell. Cell Growth Differ. 7:1996;1393-1401.
50. Skarnes WC, Moss JE, Hurtley SM, Beddington RS. Capturing genes encoding membrane and secreted proteins important for mouse development. Proc Natl Acad Sci USA. 92:1995;6592-6596.
51. Skarnes WC, Auerbach BA, Joyner AL. A gene trap approach in mouse embryonic stem cells: the lacZ reported is activated by splicing, reflects endogenous gene expression, and is mutagenic in mice. Genes Dev. 6:1992;903-918.
52. Von Melchner H, Degregori JV, Raybum H, Reddy S, Friedel C, Ruley HE. Selective disruption of genes expressed in totipotent embryonal stem cells. Genes Dev. 6:1992;919-927.
53. Chowdhury K, Bonaldo P, Torres M, Stoykova A, Gruss P. Evidence for the stochastic integration of gene trap vectors into the mouse germline. Nucleic Acids Res. 25:1997;1531-1536.
54. Hicks GG, Shi EG, Li XM, Li CH, Pawlak M, Ruley HE. Functional genomics in mice by tagged sequence mutagenesis. of special interest Nat Genet. 16:1997;338-344 Using proviral mutagenesis in mouse ES cells, a library of mutant clones was isolated and regions of genomic DNA adjacent to 400 independent provirus inserts were cloned and sequenced. The flanking sequences, designated 'promoter-proximal sequence tags', or PSTs, identified 63 specific genes and anonymous cDNAs disrupted as a result of virus integration. This method can be scaled up to give mutations in many of the genes expressed in ES cells.
55. Adams MD. Serial analysis of gene expression: ESTs get smaller. Bioessays. 18:1996;261-262.
56. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression [see comments]. Science. 270:1995;484-487.
57. Editorial: To affinity... and beyond. of special interest Nat Genet. 14:1996;367-370 An editorial reviewing and discussing the prospects for DNA microchip technology in making a significant contribution to the large-scale high throughput biology that is required to tackle the explosion in genomic data.
58. Goffeau A. DNA technology: molecular fish on chips [news]. Nature. 385:1997;202-203.
59. Lockhart DJ, Dong H, Byrne MC, Folletteie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 14:1997;1675-1680.
60. Derisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM. Use of a cDNA microarray to analyse gene expression patterns in human cancer [see comments]. Nat Genet. 14:1996;457-460.
61. Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA. 93:1996;10614-10619.
62. Schena M. Genome analysis with gene expression microarrays. Bioessays. 18:1996;427-431.
63. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray [see comments]. Science. 270:1995;467-470.
64. Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphrey Smith L, Hochstrasser DF, Williams KL. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev. 13:1996;19-50.
65. Strachan T, Abitbol M, Davidson D, Beckmann JS. A new dimension for the human genome project: towards comprehensive expression maps. of special interest Nat Genet. 16:1997;126-132 This paper reviews the current state of the Human Genome Project, which is largely devoted to structural characterisation of the human genome and addresses the need for international co-ordination of a second phase of genome analysis - the systematic construction of expression maps using both basic and high revolution expression assays. Compelling arguments are made for a database of gene expression in early human development. The scarcity of human material available for study requires optimisation of research strategies and co-ordination of expression studies in both human and mouse development.
66. Shevchenko A, Jensen ON, Podtelejnikov AV, Sagliocco F, Wilm M, Vorm O, Mortensen P, Boucherie H, Mann M. Linking genome and proteome by mass spectrometry: large scale identification of yeast proteins from two-dimensional gels. Proc Natl Acad Sci USA. 93:1996;14440-14445.
67. Chait BT. Trawling for proteins in the post-genome era. Nat Biotechnol. 14:1996;1544.
68. Fromont Racine M, Rain JC, Legrain P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens [see comments]. Nat Genet. 16:1997;277-282.