Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Wolfe, Cecily J ^a,b   Kohane, Isaac S ^a   Butte, Atul J ^a,c  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITY OF HAWAII   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CO-EXPRESSION NETWORKS; FUNCTIONAL GENOMICS; FUNCTIONAL ORGANIZATION; GUILT BY ASSOCIATIONS; INTERACTING MOLECULES; PROBABILISTIC SCORES; RECEIVER OPERATING CURVES; TRANSCRIPTIONAL CONTROL;

HEURISTIC METHODS; MAMMALS;

GENE EXPRESSION;

TRANSCRIPTOME; NEUROPEPTIDE RECEPTOR;

ANALYZER; ARTICLE; CALCULATION; CLUSTER ANALYSIS; GENE EXPRESSION; GENE FUNCTION; GENE INTERACTION; GENETIC ANALYSIS; GENETIC ASSOCIATION; INFORMATION PROCESSING; MAMMALIAN GENETICS; ONTOGENY; PROBABILITY; PROCESS DEVELOPMENT; PROCESS MODEL; REPRODUCIBILITY; SCORING SYSTEM; TRANSCRIPTION REGULATION; ANIMAL; BONE DEVELOPMENT; DNA MICROARRAY; FEEDING BEHAVIOR; GENE EXPRESSION PROFILING; GENETICS; HUMAN; MOUSE; PHYLOGENY; PHYSIOLOGY; RAT; RECEIVER OPERATING CHARACTERISTIC; SPECIES DIFFERENCE; SYNTENY;

MAMMALIA;

ANIMALS; BONE DEVELOPMENT; FEEDING BEHAVIOR; GENE EXPRESSION PROFILING; HUMANS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; PROBABILITY; RATS; RECEPTORS, NEUROPEPTIDE; REPRODUCIBILITY OF RESULTS; ROC CURVE; SPECIES SPECIFICITY; SYNTENY;

EID: 25444476441     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-227     Document Type: Article

References (24)

1. Brown, PO, Botstein, D: Exploring the new world of the genome with DNA microarrays. Nature Genet. 1999, 21:33-37.
2. Quackenbush, J: Computational analysis of microarray data. Nature Rev. Genet. 2001, 2:418-427.
3. Eisen, MB, Spellman, PT, Brown, PO, Botstein, D: Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 1998, 95:14,863-14,868.
4. Tavazoie, S, Hughes, JD, Campbell, MJ, Cho, RJ, Church, GM: Systematic determination of genetic network architecture. Nature Genet. 1999, 22:281-285.
5. Wu, LF, Hughes, TR, Davierwala, AP, Robinson, MD, Stoughton, R, Altschuler, SJ: Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nature Genet. 2002, 31:255-265.
6. Stuart, JM, Segal, E, Koller, D, Kim, SK: A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302:249-255.
7. Lee, HK, Hsu, AK, Sajdak, J, Qin, J, Pavlidis, P: Coexpression analysis of human genes across many microarray data sets. Genome Res. 2004, 14:1085-1094.
8. Hughes, TR, Marton, MJ, Jones, AR, Roberts, CJ, Stoughton, R, Armour, DC, Bennett, HA, Coffey, E, Dai, H, He, YD, Kidd, MJ, King, AM, Meyer, MR, Slade, D, Lum, PY, Stepaniants, SB, Shoemaker, DD, Gachotte, D, Chakraburtty, K, Simon, J, Bard, M, Friend, SH: Functional discovery via a compendium of expression profiles. Cell 2000, 102:109-125.
9. Ihmels, J, Friedlander, G, Bergmann, S, Sarig, O, Ziv, Y, Barkai, N: Revealing modular organization in the yeast transcriptional network. Nature Genet. 2002, 31:370-377.
10. Draghici, S, Khatri, P, Martins, RP, Charles Ostermeier, G, Krawetz, SA: Global functional profiling of gene expression. Genomics 2003, 81:98-104.
11. Lamb, JA, Ramaswamy, S, Ford, HL, Contreras, B, Martinez, RV, Kittrell, FS, Zahnow, CA, Patterson, N, Golub, TR, Ewen, ME: A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer. Cell 2003, 114:323-334.
12. Mootha, VK, Lindgren, CM, Eriksson, KF, Subramanian, A, Sihag, S, Lehar, J, Puigserver, P, Carlsson, E, Ridderstrale, M, Laurila, E, Houstis, N, Daly, MJ, Patterson, N, Mesirov, JP, Golub, TR, Tamayo, P, Spiegelman, B, Lander, ES, Hirschhorn, JN, Altshuler, D, Groop, LC: PGC-1 Alpha-responsive genes involve in oxidative phosphorylation are coordinately downregulated in human diabetes. Nature Genet. 2003, 34:267-273.
13. McCarroll, SA, Murphy, CT, Zou, S, Pletcher, SD, Chin, CS, Jan, YN, Kenyon, C, Bargmann, CI, Li, H: Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nature Genet. 2004, 36:197-204.
14. Segal, E, Friedman, N, Koller, D, Regev, A: A module map showing conditional activity of expression modules in cancer. Nature Genet. 2004, 36:1090-1098.
15. Sweet-Cordero, A, Mukherjee, S, Subramanian, A, You, H, Roix, JJ, Ladd-Acosta, C, Mesirov, J, Golub, TR, Jacks, T: An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nature Genet. 2004, 37:48-55.
16. Fraser, AG, Marcotte, EM: A probabilistic view of gene function. Nature Genet. 2004, 36:559-564.
17. 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: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25:25-29.
18. Bittner, M, Meltzer, P, Trent, J: Data analysis and integration: of steps and arrows. Nature Genet. 1999, 22:213-215.
19. Jeffrey, C: Moonlighting proteins. Trends Biochem. Sci. 1999, 24:8-11.
20. Hanley, JA, McNeil, BJ: The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 1982, 143:29-36.
21. Members of the Toxicogenomics Research Consortium: Standardizing global gene expression analysis between laboratories and across platforms, Nat. Methods 2005, 2:351-365.
22. Zhang, W, Morris, GQ, Chang, R, Shai, O, Bakowski, MA, Mitsakakis, N, Mohammad, N, Robinson, MD, Zirngibl, R, Somogvi, E, Laurin, N, Eftekharpour, E., Sat, E, Grigull, J, Pan, Q, Peng, WT, Krogan, N, Greenblatt, J, Fehlings, M, van der Kooy, D, Aubin, J, Bruneau, GB, Rossant, J, Blencowe, BJ, Frey, BJ, Hughes, TR: The functional landscape of mouse gene expression, J. Biol. 2004, 3:21.
23. Clare, A, King, RD: How well do we understand the clusters found in microarray data? In Silico Biol. 2002, 2:0046.
24. Hartwell, LH, Hopfield, JJ, Leibler, S, Murray, AW: From molecular to modular cell biology. Nature 1999, 402:C47-C52.