Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Biswas, Shameek ^a   Storey, John D ^a   Akey, Joshua M ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIMENSION REDUCTION METHOD; DIMENSION REDUCTION TECHNIQUES; EXPRESSION VARIATIONS; GENE EXPRESSION PROFILING; GENETIC ARCHITECTURE; INDEPENDENT COMPONENT ANALYSIS(ICA); LINEAR COMBINATIONS; QUANTITATIVE TRAIT LOCUS;

INDEPENDENT COMPONENT ANALYSIS; PLANTS (BOTANY); SINGULAR VALUE DECOMPOSITION; YEAST;

GENE EXPRESSION;

ARTICLE; CONTROLLED STUDY; FUNGAL GENETICS; FUNGAL METABOLISM; FUNGAL STRAIN; GENE EXPRESSION; INDEPENDENT COMPONENT ANALYSIS; ION TRANSPORT; LINKAGE ANALYSIS; MULTIVARIATE ANALYSIS; NONHUMAN; QUANTITATIVE TRAIT LOCUS MAPPING; RETROPOSON; RNA PROCESSING; SACCHAROMYCES CEREVISIAE; SINGULAR VALUE DECOMPOSITION; STATISTICAL ANALYSIS; TELOMERE; CHROMOSOME MAP; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; GENETICS; METHODOLOGY; PRINCIPAL COMPONENT ANALYSIS; QUANTITATIVE TRAIT LOCUS;

SACCHAROMYCES CEREVISIAE;

CHROMOSOME MAPPING; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; PRINCIPAL COMPONENT ANALYSIS; QUANTITATIVE TRAIT LOCI; VARIATION (GENETICS);

EID: 45249095384     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-244     Document Type: Article

References (44)

1. Brem RB Yvert G Clinton R Kruglyak L Genetic dissection of transcriptional regulation in budding yeast Science 2002 296 752-755 10.1126/science.1069516 11923494
2. Cheung VG Conlin LK Weber TM Arcaro M Jen KY Morley M Spielman RS Natural variation in human gene expression assessed in lymphoblastoid cells Nature Genet 2003 33 422-425 10.1038/ng1094 12567189
3. Schadt EE Monks SA Drake TA Lusis AJ Che N Colinayo V Ruff TG Milligan SB Lamb JR Cavet G Linsley PS Mao M Stoughton RB Friend SH Genetics of gene expression surveyed in maize, mouse and man Nature 2003 422 297-302 10.1038/nature01434 12646919
4. Monks SA Leonardson A Zhu H Cundiff P Pietrusiak P Edwards S Phillips JW Sachs A Schadt EE Genetic inheritance of gene expression in human cell lines Am J Hum Genet 2004 75 1094-1105 1182144 15514893 10.1086/426461
5. Morley M Molony CM Weber TM Devlin JL Ewens KG Spielman RS Cheung VG Genetic analysis of genome-wide variation in human gene expression Nature 2004 430 743-747 10.1038/nature02797 15269782
6. Bing N Hoeschele I Genetical Genomics Analysis of a Yeast Segregant Population for Transcription Network Inference Genetics 2005 170 533-542 1450429 15781693 10.1534/genetics.105.041103
7. Jansen RC Nap JP Genetical genomics: The added value from segregation Trends Genet 2001 17 388-391 10.1016/S0168-9525(01)02310-1 11418218
8. Yvert G Brem RB Whittle J Akey JM Foss E Smith EN Mackelprang R Kruglyak L Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors Nature Genet 2003 35 57-64 10.1038/ng1222 12897782
9. Golub GH Van Loan CF Matrix Computation Baltimore: Johns Hopkins Univ. Press 1996
10. Alter O Brown PO Botstein D Singular value decomposition for genome-wide expression data processing and modeling Proc Natl Acad Sci 2000 97 10101 10106 27718 10963673 10.1073/pnas.97.18.10101
11. Hyvarinen A Oja E Independent Component Analysis: Algorithms and Applications Neural Networks 2000 13 411-430 10.1016/ S0893-6080(00)00026-5 10946390
12. Baek K Draper B Beveridge J She K PCA vs ICA: A comparison on the FERET data set Joint Conference on Information Sciences 2002
13. Bartlett MS Movellan JR Sejnowski TJ Face recognition by independent component analysis IEEE Trans. on Neural Networks 2002 13 1450-1464 10.1109/TNN.2002.804287
14. Hastie T Tibshirani R Friedman J Unsupervised Learning The Elements of Statistical Learning New York: Springer-Verlag 1 2001 485-501
15. Teschendorff AE Journee M Absil P Sepulchre R Caldas C Elucidating the altered transcriptional programs in breast cancer using independent component analysis PLoS Computational Biology 2007 3 e161 1950343 17708679 10.1371/journal.pcbi.0030161
16. Yeung KY Ruzzo WL Principal component analysis for clustering gene expression data Bioinformatics 2001 17 763-774 10.1093/bioinformatics/ 17.9.763 11590094
17. Misra J Schmitt W Hwang D Hsiao L Gullans S Stephanopoulos G Stephanopoulos G Interactive Exploration of Microarray Gene Expression Patterns in a Reduced Dimensional Space Genome Research 2002 12 1112-1120 186614 12097349 10.1101/gr.225302
18. Lee S Batzoglou S Application of independent component analysis to microarrays Genome Biology 2003 4 R76 329130 14611662 10.1186/ gb-2003-4-11-r76
19. Frigyesi A Veerla S Lindgren D Hoglund M Independent component analysis reveals new and biologically significant structures in micro array data BMC Bioinformatics 2006 7 290-302 1557674 16762055 10.1186/ 1471-2105-7-290
20. Alter O Brown PO Botstein D Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms Proc Natl Acad Sci 2003 100 3351-3356 152296 12631705 10.1073/pnas.0530258100
21. Raychaudhuri S Stuart JM Altman RB Principal components analysis to summarize microarray experiments: Application to sporulation time series Pacific Symposium on Biocomputing 2000 455-466 10902193
22. Carter GW Rupp S Fink GR Galitski T Disentangling information flow in the Ras-cAMP signaling network Genome Res 2006 16 520-526 1457029 16533914 10.1101/gr.4473506
23. Nielsen TO West RB Linn SC Alter O Knowling MA O'Connell JX Zhu S Fero M Sherlock G Pollack JR Brown PO Botstein D Rijn Van De M Molecular characterisation of soft tissue tumours: A gene expression study Lancet 2002 359 1301-1307 10.1016/S0140-6736(02)08270-3 11965276
24. Shen R Ghosh D Chinnaiyan A Meng Z Eigengene based linear discriminant model for tumor classification using gene expression microarray data Bioinformatics 2006 22 2635-2642 10.1093/bioinformatics/btl442 16926220
25. Zhang XW Yap YL Wei D Chen F Danchin A Molecular diagnosis of human cancer type by gene expression profiles and independent component analysis Eur J Hum Genet 2005 13 1303-1311 10.1038/sj.ejhg.5201495 16205741
26. Chiappetta P Roubaud MC Torresani R Blind Source Separation and the Analysis of Microarray Data Journal of Computational Biology 2004 11 1090-1109 10.1089/cmb.2004.11.1090 15662200
27. Lan H Stoehr JP Nadler ST Schueler KL Yandell BS Attie AD Dimension Reduction for Mapping mRNA Abundance as Quantitative Traits Genetics 2003 164 1607-1614 1462655 12930764
28. Bensen JT Lange LA Langefeld CD Chang BL Bleecker ER Meyers DA Xu J Exploring pleiotropy using principal components BMC Genet 2003 4 S53 1866490 14975121 10.1186/1471-2156-4-S1-S53
29. Gilbert H Le Roy P Comparison of three multitrait methods for QTL detection Genet Sel Evol 2003 35 281-304 10.1051/gse:2003009 12729550
30. Ghazalpour A Doss S Sheth SS Ingram-Drake LA Schadt EE Lusis AJ Drake TA Genomic analysis of metabolic pathway gene expression in mice Genome Biol 2005 6 R59 1175990 15998448 10.1186/gb-2005-6-7-r59
31. Brem RB Kruglyak L The landscape of genetic complexity across 5,700 gene expression Proc Natl Acad Sci 2005 102 1572-1577 547855 15659551 10.1073/ pnas.0408709102
32. Lynch M Walsh B Genetics and Analysis of Quantitative Traits Sunderland, MA: Sinauer Associates 1998
33. Storey JD Tibshirani R Statistical significance for genomewide studies Proc Natl Acad Sci 2003 100 9440-9445 170937 12883005 10.1073/ pnas.1530509100
34. Liebermeister W Linear modes of gene expression determined by independent component analysis Bioinformatics 2002 18 51-60 10.1093/ bioinformatics/18.1.51 11836211
35. Berriz GF King OD Bryant B Sander C Roth FP Characterizing gene sets with FuncAssociate Bioinformatics 2003 19 2502-2504 10.1093/ bioinformatics/btg363 14668247
36. Churchill GA Doerge RW Empirical threshold values for quantitative trait mapping Genetics 1994 138 963-971 1206241 7851788
37. Fungal Genome Initiative http://www.broad.mit.edu/annotation/fgi/
38. Dunn B Levine RP Sherlock G Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures BMC Genomics 2005 6 53 1097725 15833139 10.1186/1471-2164-6-53
39. Kerr MK Martin M Churchill GA Analysis of variance for gene expression microarray data J Comput Biol 2000 7 819-837 10.1089/10665270050514954 11382364
40. Horn JL A rationale and test for the number of factors in factor analysis Psychometrika 1965 30 179-185 10.1007/BF02289447 14306381
41. R Development Core Team R: A Language and Environment for Statistical Computing R Foundation for Statistical Computing, Vienna, Austria 2006 http://www.R-project.org [ISBN 3-900051-07-0].
42. Marchini J Heaton C fastICA: FastICA algorithms to perform ICA and Projection Pursuit 2006 http://www.stats.ox.ac.uk/~marchini/ software.html [R package version 1.1-8.]
43. Teschendorff A MLICA: Independent Component Analysis using Maximum Likelihood [R package version 0.6].
44. Broman KW Wu H QTL: Tools for analyzing QTL experiments 2006 http://www.rqtl.org with ideas from Gary Churchill, Sen S, contributions from Brian Yandell [R package version 1.04-53].