Analysis of SNP-expression association matrices

Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005

Volumn 2005, Issue , 2005, Pages 135-143

  Tsalenko, Anya ^a   Sharan, Roded ^b   Edvardsen, Hege ^c   Kristensen, Vessela ^c   Børresen Dale, Anne Lise ^c   Ben Dor, Amir ^a   Yakhini, Zohar ^a  

^a AGILENT TECHNOLOGIES   (United States)

^b TEL AVIV UNIVERSITY   (Israel)

^c UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; COMPUTER SIMULATION; DATA STRUCTURES; GENES; GENETIC ALGORITHMS; MATRIX ALGEBRA; SET THEORY;

GENE EXPRESSION DATA; GENOTYPING TECHNOLOGIES; SNP-EXPRESSION; TRANSCRIPTION;

GENETIC ENGINEERING;

TUMOR MARKER; TUMOR PROTEIN;

ALGORITHM; ARTICLE; BREAST TUMOR; CHROMOSOME MAP; COMPUTER INTERFACE; EVALUATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETICS; GENOTYPE; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; BREAST NEOPLASMS; CHROMOSOME MAPPING; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOTYPE; NEOPLASM PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; TUMOR MARKERS, BIOLOGICAL; USER-COMPUTER INTERFACE;

EID: 33745505569     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CSB.2005.14     Document Type: Conference Paper

References (21)

1. Ben-Dor, A, Friedman N, and Yakhini Z. (2001) "Class Discovery in Gene Expression Data." Proceedings of the Fifth International Conference on Computational Biology RECOMB'01: 31-38.
2. Benjamini Y, Hochberg Y (1995) "Controlling the false discovery rate- a practical and powerful approach to multiple testing", J Roy Stat Soc B Met 57(1), p289-300.
3. Brem RB, Yvert G, Clinton R, Kruglyak L. (2002) "Genetic dissection of transcriptional regulation in budding yeast". Science. 26;296(5568), p752-5.
4. Chen MM, Ashley EA, Deng DX, Tsalenko A, Deng A, Tabibiazar R, Ben-Dor A, Fenster B, Yang E, King JY, Fowler M, Robbins R, Johnson FL, Bruhn L, McDonagh T, Dargie H, Yakhini Z, Tsao PS, Quertermous T. (2003) "Novel role for the potent endogenous inotrope apelin in human cardiac dysfunction". Circulation, vol.108.
5. Gao F, Foat B, and Bussemaker H. "Defining transcriptional networks through integrative modeling of mRNA expression and transcriptional factor binding data" BMC Bioinformatics (2004), 5:31.
6. Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R, Meltzer P, Gusterson B, Esteller M, Kallioniemi OP, Wilfond B, Borg A, Trent J. (2001) "Gene-expression profiles in hereditary breast cancer". N Engl J Med. 344(8):p539-48.
7. Hedenfalk I, Ringner M, Ben-Dor A, Yakhini Z, Chen Y, Chebil G, Ach R, Loman N, Olsson H, Meltzer P, Borg A, Trent J. (2003) "Molecular classification of familial non-BRCA1/BRCA2 breast cancer". Proc Natl Acad Sci USA. 100(5):p2532-7.
8. Ho M, Yang E, Matcuk G, Deng D, Sampas N, Tsalenko A, Tabibiazar R, Zhang Y, Chen M, Talbi S, Ho YD, Wang J, Tsao PS, Ben-Dor A, Yakhini Z, Bruhn L, Quertermous T. (2003) "Identification of endothelial cell genes by combined database mining and microarray analysis" Physiol Genomics. vol. 13(3).
9. Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, Gibson G. (2001) "The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster". Nat Genet. 29(4), p389-95.
10. Kincaid R, Kleusing, D, Vailaya, A (2002) "BNS: An LDAP-based Biomolecule Naming Service." OiBC. Washington DC.
11. Kristensen V, Edvardsen H, Nordgard S, Sørlie T, Lønning PE, Lien S, Omholt S, Syvanen AC, Tsalenko A, Ben-Dor A, Yakhini Z and Børresen-Dale AL. "Potential master regulators of gene expression cancer related pathways", in preparation to be submitted.
12. Martin D, Brun C, Remy E, Mouren P, Thieffry D and Jacq B. (2004) "GOToolBox: functional analysis of gene datasets based on Gene Ontology" Genome Biology, 5:R101.
13. Morley M, Molony C, Weber T, Devlin J, Ewens K, Spielman R and Cheung V, (2004) "Genetic analysis of genome-wide variation in human gene expression", Nature, vol.430.
14. Rice J. (1995) Mathematical Statistics and Data Analysis. Duxbury Press.
15. Sandberg R, Yasuda R, Pankratz DG, Carter TA, Del Rio JA, Wodicka L, Mayford M, Lockhart DJ, & Barlow C. (2000) "Regional and strain-specific gene expression mapping in the adult mouse brain". Proc. Natl. Acad. Sci. USA 97, 11038-43.
16. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TO, Milligan SB, Lamb JR, Cavet G, Linsley PS, Mao M, Stoughton RB, Friend SH. (2003) "Genetics of gene expression surveyed in maize, mouse and man", Nature, 422(6929):p297-302.
17. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Eystein Lonning P, Borresen-Dale AL. (2001) "Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications" Proc Natl Acad Sci USA. 98: p10869-74.
18. Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, Demeter J, Perou CM, Lonning PE, Brown PO, Borresen-Dale AL, Botstein D. (2003) "Repeated observation of breast tumor subtypes in independent gene expression data sets". Proc Natl Acad Sci USA 100: p8418-23.
19. Tanay A, Sharan R, Kupiec M and Shamir R. (2004) "Revealing Modularity and Organization in the Yeast Molecular Network by Integrated Analysis of Highly Heterogeneous Genome-wide Data", Proc. Natl, Acad. Sci. USA 101:p2981-2986.
20. Tsalenko A, Ben-Dor A, Cox N, Yakhini Z. (2003) "Methods for analysis and visualization of SNP genotype data for complex diseases". Pac Symp Biocomput.; p548-61.
21. Watts JA, Morley M, Burdick JT, Fiori JL, Ewens WJ, Spielman RS, Cheung VG. (2002) "Gene expression phenotype in heterozygous carriers of ataxia telangiectasia", Am J Hum Genet. 71(4):p791-800.