Effective similarity measures for expression profiles

Bioinformatics

Volumn 22, Issue 13, 2006, Pages 1616-1622

  Yona, Golan ^a,b,c   Dirks, William ^b   Rahman, Shafquat ^a   Lin, David M ^b  

^a Department of Computer Science and School of Operations Research and Information Engineering   (United States)

^b Department of Obstetrics Gynecology   (United States)

^c TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL METABOLISM; COMPARATIVE STUDY; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENE FUNCTION; GENETIC DISTANCE; GENETIC LINKAGE; INTERNET; MOLECULAR PHYLOGENY; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN INTERACTION; SCORING SYSTEM; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS;

EID: 33745601692     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl127     Document Type: Article

References (19)

1. Bammer,G. and Fostel,J. (2000) Genome-wide expression patterns in Saccharomyces cerevisiae: Comparison of drug treatments and genetic alterations affecting biosynthesis of ergosterol. Antimicrob. Agents Chemother., 44, 1255-1265.
2. Birkland,A. and Yona,G. (2006) The BIOZON Database: A hub of heterogeneous biological data. Nucleic Acids Res., 34, D235-D242.
3. Cho,R.J. et al. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2, 65-73.
4. Diffee,G.M. et al., Seversen,E.A., Stein,T.D. and Johnson,J.A. (2003) Microarray expression analysis of effects of exercise training: Increase in atrial MLC-1 in rat ventricle Am. J. Physiol. Heart Circ. Physiol., 284, H830-H837.
5. Gasch,A.P. et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell, 11, 4241-4257.
6. Gygi,S.P. et al. (1999) Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol., 19, 1720-1730.
7. Hanley,J.A. and McNeil,B.J. (1982) The meaning and use of the area under the Receiver Operating Characteristic (ROC) curve. Radiology, 143, 29-36.
8. Hughes,T. et al. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109-126.
9. Liu,E.T. (2003) Classification of cancers by expression profiling. Curr. Opin. Genet. Dev., 13, 97-103.
10. Lopez,I.P. et al. (2003) DNA microarray analysis of genes differentially expressed in diet-induced (cafeteria) obese rats. Obes. Res., 11, 188-194.
11. McCormick,S.M. et al. (2003) Microarray analysis of shear stressed endothelial cells. Biorheology, 40, 5-11.
12. Miklos,G. and Rubin,G. (1996) The role of the genome project in determining gene function: Insights from model organisms. Cell, 86, 521-529.
13. Popescu,L. and Yona,G. (2005) Automation of gene assignments to metabolic pathways using high-throughput expression data. BMC Bioinformatics, 6, 217.
14. Qian,J. et al. (2001) Beyond synexpression relationships: Local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions. J. Mol. Biol., 312, 1053-1066.
15. Shapira,M. et al. (2004) Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. Mol. Biol. Cell, 15, 5659-5669.
16. Spellman,P.T. et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
17. Algorithm AS 89. (1975) Tail probabilities for Spearman's rho. Applied Statistics algorithms, 24, 377.
18. Yeatman,T.J. (2003) The future of clinical cancer management: One tumor, one chip. Am. Surg., 69, 41-44.
19. Yoo,M.S. et al. (2003) Oxidative stress regulated genes in nigral dopaminergic neurnol cell: Correlation with the known pathology in Parkinson's disease. Brain Res. Mol. Brain Res., 110, 76-84.