A gene recommender algorithm to identify coexpressed genes in C. elegans

Genome Research

Volumn 13, Issue 8, 2003, Pages 1828-1837

  Owen, Art B ^a   Stuart, Josh ^a,b   Mach, Kathy ^b   Villeneuve, Anne M ^b   Kim, Stuart ^b  

^a STANFORD UNIVERSITY   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HELMINTH DNA;

ACCURACY; ALGORITHM; ARTICLE; CAENORHABDITIS ELEGANS; CELL FATE; CONTROLLED STUDY; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENETICS; GENOME; NONHUMAN; PRIORITY JOURNAL; RETINOBLASTOMA;

ALGORITHMS; ANIMALS; CAENORHABDITIS ELEGANS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA, HELMINTH; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES, HELMINTH; GENES, RETINOBLASTOMA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA INTERFERENCE; SOFTWARE;

CAENORHABDITIS; CAENORHABDITIS ELEGANS; INVERTEBRATA; NEMATODA; VERMES;

EID: 0042024906     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (43)

1. Bhat, U.G., Raychaudhuri, P., and Beck, W.T. 1999. Functional interaction between human topoisomerase IIα and retinoblastoma protein. Proc. Natl. Acad. Sci. 96: 7859-7864.
2. Brown, P.O. and Botstein, D. 1999. Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21: 33-37.
3. The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282: 2012-2018.
4. Ceol, C.J. and Horvitz, H.R. 2001. dpl-1 DP and efl-1 E2F act with lin-35 Rb to antagonize Ras signaling in C. elegans vulval development. Mol. Cell 7: 461-473.
5. Chase, D., Serafinas, C., Ashcroft, N., Kosinski, M., Longo, D., Ferris, D.K., and Golden, A. 2000. The polo-like kinase PLK-1 is required for nuclear envelope breakdown and the completion of meiosis in Caenorhabditis elegans. Genesis 26: 26-41.
6. Dyson, N. 1998. The regulation of E2F by pRB-family proteins. Genes & Dev. 12: 2245-2262.
7. Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. 95: 14863-14868.
8. Eisenmann, D.M., Maloof, J.N., Simske, J.S., Kenyon, C., and Kim, S.K. 1998. The β-catenin homolog BAR-1 and LET-60 Ras coordinately regulate the Hox gene lin-39 during Caenorhabditis elegans vulval development. Development 125: 3667-3680.
9. Ferguson, E.L. and Horvitz, H.R. 1989. The multivulva phenotype of certain Caenorhabditis elegans mutants results from defects in two functionally redundant pathways. Genetics 123: 109-121.
10. Fraser, A.G., Kamath, R.S., Zipperlen, P., Martinez-Campos, M., Sohrmann, M., and Ahringer, J. 2000. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408: 325-330.
11. Friedman, J.H. and Meulman, J.J. 2002. Clustering objects on susbets of attributes. Technical Report, Stanford University, Statistics.
12. Gasch, A.P. and Eisen, M.B. 2002. Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol. 3: RESEARCH0059.1-RESEARCH0059.22.
13. Hagstrom, K.A., Holmes, V.F., Cozzarelli, N.R., and Meyer, B.J. 2002. C. elegans condensin promotes mitotic chromosome architecture, centromere organization, and sister chromatid segregation during mitosis and meiosis. Genes & Dev. 16: 729-742.
14. Hauser, B.A., He, J.Q., Park, S.O., and Gasser, C.S. 2000. TSO1 is a novel protein that modulates cytokinesis and cell expansion in Arabidopsis. Development 127: 2219-2226.
15. Hughes, T.R., Marton, M.J., Jones, A.R., Roberts, C.J., Stoughton, R., Armour, C.D., Bennett, H.A., Coffey, E., Dai, H., He, Y.D., et al. 2000. Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
16. Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y., and Barkai, N. 2002. Revealing modular organization in the yeast transcriptional network. Nat. Genet. 31: 370-377.
17. Jiang, M., Ryu, J., Kiraly, M., Duke, K., Reinke, V., and Kim, S.K. 2001. Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proc. Natl. Acad. Sci. 98: 218-223.
18. Kim, S.K. 2001. Http://C. elegans: Mining the functional genomic landscape. Nat. Rev. Genet. 2: 681-689.
19. Kim, S.K., Lund, J., Kiraly, M., Duke, K., Jiang, M., Wylie, B.N., and Davidson, G.S. 2001. A gene expression map for C. elegans. Science 293: 2087-2092.
20. Kornfeld, K. 1997. Vulval development in Caenorhabditis elegans. Trends Genet. 13: 55-61.
21. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
22. Lu, X. and Horvitz, H.R. 1998. lin-35 and lin-53, two genes that antagonize a C. elegans Ras pathway, encode proteins similar to Rb and its binding protein RbAp48. Cell 95: 981-991.
23. Lund, J., Tedesco, P., Duke, K., Wang, J., Kim, S.K., and Johnson, T.E. 2002. Transcriptional profile of aging in C. elegans. Curr. Biol. 12: 1566-1573.
24. Mateos, A., Dopazo, J., Jansen, R., Tu, Y., Gerstein, M., and Stolovitzky, G. 2002. Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons. Genome Res. 12: 1703-1715.
25. Myers, E.W., Sutton, G.G., Delcher, A.L., Dew, I.M., Fasulo, D.P., Flanigan, M.J., Kravitz, S.A., Mobarry, C.M., Reinert, K.H., Remington, K.A., et al. 2000. A whole-genome assembly of Drosophila. Science 287: 2196-2204.
26. Nusse, R., van Ooyen, A., Cox, D., Fung, Y.K., and Varmus, H. 1984. Mode of proviral activation of a putative mammary oncogene (int-1) on mouse chromosome 15. Nature 307: 131-136.
27. Oegema, K., Desai, A., Rybina, S., Kirkham, M., and Hyman, A.A. 2001. Functional analysis of kinetochore assembly in Caenorhabditis elegans. J. Cell. Biol. 153: 1209-1226.
28. Pavlidis, P., Lewis, D.P., and Noble, W.S. 2002. Exploring gene expression data with class scores. Pac. Symp. Biocomput.: 474-485.
29. Piano, F., Schetter, A.J., Morton, D.G., Gunsalus, K.C., Reinke, V., Kim, S.K., and Kemphues, K.J. 2002. Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr. Biol. 12: 1959-1964.
30. Reinke, V., Smith, H.E., Nance, J., Wang, J., Van Doren, C., Begley, R., Jones, S.J., Davis, E.B., Scherer, S., Ward, S., et al. 2000. A global profile of germline gene expression in C. elegans. Mol. Cell 6: 605-616.
31. Rocheleau, C.E., Yasuda, J., Shin, T.H., Lin, R., Sawa, H., Okano, H., Priess, J.R., Davis, R.J., and Mello, C.C. 1999. WRM-1 activates the LIT-1 protein kinase to transduce anterior/posterior polarity signals in C. elegans. Cell 97: 717-726.
32. Rowley, A., Singer, R.A., and Johnston, G.C. 1991. CDC68, a yeast gene that affects regulation of cell proliferation and transcription, encodes a protein with a highly acidic carboxyl terminus. Mol. Cell. Biol. 11: 5718-5726.
33. Roy, P.J., Stuart, J.M., Lund, J., and Kim, S.K. 2002. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418: 975-979.
34. Schaller, A., Martin, F., and Muller, B. 1997. Characterization of the calf thymus hairpin-binding factor involved in histone pre-mRNA 3′ end processing. J. Biol. Chem. 272: 10435-10441.
35. Solari, F. and Ahringer, J. 2000. NURD-complex genes antagonize Ras-induced vulval development in Caenorhabditis elegans. Curr. Biol. 10: 223-226.
36. Song, J.Y., Leung, T., Ehler, L.K., Wang, C., and Liu, Z. 2000. Regulation of meristem organization and cell division by TSO1, an Arabidopsis gene with cysteine-rich repeats. Development 127: 2207-2217.
37. Sterner, J.M., Dew-Knight, S., Musahl, C., Kornbluth, S., and Horowitz, J.M. 1998. Negative regulation of DNA replication by the retinoblastoma protein is mediated by its association with MCM7. Mol. Cell. Biol. 18: 2748-2757.
38. Sugihara, T., Wadhwa, R., Kaul, S.C., and Mitsui, Y. 1999. A novel testis-specific metallothionein-like protein, tesmin, is an early marker of male germ cell differentiation. Genomics 57: 130-136.
39. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A., et al. 2001. The sequence of the human genome. Science 291: 1304-1351.
40. Walhout, A.J., Reboul, J., Shtanko, O., Bertin, N., Vaglio, P., Ge, H., Lee, H., Doucette-Stamm, L., Gunsalus, K.C., Schetter, A.J., et al. 2002. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr. Biol. 12: 1952-1958.
41. Wang, J. and Kim, S.K. 2003. Global analysis of dauergene expression in Caenorhabditis elegans. Development 130: 1621-1634.
42. Willert, K. and Nusse, R. 1998. β-catenin: A key mediator of Wnt signaling. Curr. Opin. Genet. Dev. 8: 95-102.
43. Yeung, K.Y., Haynor, D.R., and Ruzzo, W.L. 2001. Validating clustering for gene expression data. Bioinformatics 17: 309-318.