Statistical methods for the analysis of the genetics of gene expression
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[1] V. Zídek,et al. Genetic isolation of a chromosome 1 region affecting blood pressure in the spontaneously hypertensive rat. , 1997, Hypertension.
[2] 김동일,et al. LARS(Least Angle Regression)와 유전알고리즘을 결합한 변수 선택 알고리즘 , 2009 .
[3] N. Yi,et al. Bayesian LASSO for Quantitative Trait Loci Mapping , 2008, Genetics.
[4] Daniel Levy,et al. Long-term trends in the incidence of and survival with heart failure. , 2002, The New England journal of medicine.
[5] D. Clayton,et al. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region , 2006, Nature Genetics.
[6] V. Zídek,et al. Chromosomal mapping of a major quantitative trait locus regulating compensatory renal growth in the rat. , 2000, Journal of the American Society of Nephrology : JASN.
[7] D. Simmons,et al. Molecular cloning of CD68, a human macrophage marker related to lysosomal glycoproteins. , 1993, Blood.
[8] H. Mcdevitt,et al. Interferon-α initiates type 1 diabetes in nonobese diabetic mice , 2008, Proceedings of the National Academy of Sciences.
[9] R. Khalil,et al. Gender, sex hormones, and vascular tone. , 2004, American journal of physiology. Regulatory, integrative and comparative physiology.
[10] John A. Todd,et al. Statistical independence of the colocalized association signals for type 1 diabetes and RPS26 gene expression on chromosome 12q13 , 2008, Biostatistics.
[11] E. Lander. The New Genomics: Global Views of Biology , 1996, Science.
[12] H. Ropers. New perspectives for the elucidation of genetic disorders. , 2007, American journal of human genetics.
[13] S. Mccune,et al. Plasma renin activity in heart failure-prone SHHF/Mcc-facp rats. , 1997, The American journal of physiology.
[14] K. Gunderson,et al. Illumina universal bead arrays. , 2006, Methods in enzymology.
[15] M. Herrath. Diabetes: A virus–gene collaboration , 2009, Nature.
[16] C. Haley,et al. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers , 1992, Heredity.
[17] L. Penrose,et al. THE CORRELATION BETWEEN RELATIVES ON THE SUPPOSITION OF MENDELIAN INHERITANCE , 2022 .
[18] Rafael A Irizarry,et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.
[19] D. Rubin,et al. The central role of the propensity score in observational studies for causal effects , 1983 .
[20] Andrew B. Nobel,et al. Significance analysis of functional categories in gene expression studies: a structured permutation approach , 2005, Bioinform..
[21] H. Akaike. A new look at the statistical model identification , 1974 .
[22] Marit Holden,et al. GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies , 2008, Bioinform..
[23] M. Vingron,et al. Quantifying the effect of sequence variation on regulatory interactions , 2010, Human mutation.
[24] D. Kelly,et al. Fatty acid oxidation enzyme gene expression is downregulated in the failing heart. , 1996, Circulation.
[25] Alexander E. Kel,et al. TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..
[26] Wei Li. Analyzing Gene Expression Data in Terms of Gene Sets: Gene Set Enrichment Analysis , 2009 .
[27] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[28] M. Soller,et al. The Efficiency of Experimental Designs for the Detection of Linkage between a Marker Locus and a Locus Affecting a Quantitative Trait in Segregating Populations , 1978 .
[29] Nathan Mantel,et al. Chi-square tests with one degree of freedom , 1963 .
[30] P Klír,et al. An analysis of spontaneous hypertension in spontaneously hypertensive rats by means of new recombinant inbred strains. , 1989, Journal of hypertension.
[31] G. Box. NON-NORMALITY AND TESTS ON VARIANCES , 1953 .
[32] M. Metzker. Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.
[33] Robert Pavur,et al. A new statistic in the one-way multivariate analysis of variance , 1985 .
[34] Chester L. Olson,et al. Comparative Robustness of Six Tests in Multivariate Analysis of Variance , 1974 .
[35] A. Monaco,et al. Isolation of candidate cDNAs for portions of the Duchenne muscular dystrophy gene , 1986, Nature.
[36] Amos Tanay,et al. Extensive low-affinity transcriptional interactions in the yeast genome. , 2006, Genome research.
[37] L. Kruglyak,et al. Genetic Dissection of Transcriptional Regulation in Budding Yeast , 2002, Science.
[38] T. Kurtz,et al. Genetic analysis of metabolic defects in the spontaneously hypertensive rat , 2002, Mammalian Genome.
[39] E. Blasi,et al. Structural, functional, and molecular characterization of the SHHF model of heart failure. , 2002, American journal of physiology. Heart and circulatory physiology.
[40] R. Jansen,et al. Interval mapping of multiple quantitative trait loci. , 1993, Genetics.
[41] J. Naylor,et al. Mendelian inheritance in man: A catalog of human genes and genetic disorders , 1996 .
[42] R. Tibshirani. The lasso method for variable selection in the Cox model. , 1997, Statistics in medicine.
[43] J. Ibrahim,et al. Genomewide Multiple-Loci Mapping in Experimental Crosses by Iterative Adaptive Penalized Regression , 2010, Genetics.
[44] Kimberly A. Smith,et al. POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer , 2004, Genome Biology.
[45] Eleazar Eskin,et al. A sequence-based variation map of 8.27 million SNPs in inbred mouse strains , 2007, Nature.
[46] N. Schork,et al. Accommodating linkage disequilibrium in genetic-association analyses via ridge regression. , 2008, American journal of human genetics.
[47] M. Spence,et al. Heart Rate and Blood Pressure Quantitative Trait Loci for the Airpuff Startle Reaction , 2002, Hypertension.
[48] Matthias Heinig,et al. New Insights into the Genetic Control of Gene Expression using a Bayesian Multi-tissue Approach , 2010, PLoS Comput. Biol..
[49] Franklin A. Graybill,et al. Theory and Application of the Linear Model , 1976 .
[50] C. Priebe,et al. A weighted generalization of the Mann-Whitney-Wilcoxon statistic , 2002 .
[51] Martin Vingron,et al. Predicting transcription factor affinities to DNA from a biophysical model , 2007, Bioinform..
[52] Z. Zeng. Precision mapping of quantitative trait loci. , 1994, Genetics.
[53] J. Monod,et al. Genetic regulatory mechanisms in the synthesis of proteins. , 1961, Journal of Molecular Biology.
[54] Vladimir Svetnik,et al. STATISTICAL ANALYSIS OF HIGH DENSITY OLIGONUCLEOTIDE ARRAYS: A SAFER APPROACH , 2001 .
[55] Nicola J. Rinaldi,et al. Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.
[56] Ed Anderson,et al. LAPACK Users' Guide , 1995 .
[57] N Risch,et al. The Future of Genetic Studies of Complex Human Diseases , 1996, Science.
[58] Inanç Birol,et al. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. , 2010, Genome research.
[59] D. Balding,et al. Handbook of statistical genetics , 2004 .
[60] A J Belanger,et al. Epidemiology of heart failure. , 1991, American heart journal.
[61] Jingyuan Fu,et al. Genetical Genomics: Spotlight on QTL Hotspots , 2008, PLoS genetics.
[62] Trevor Hastie,et al. The Elements of Statistical Learning , 2001 .
[63] P. Baker,et al. SHHF/Mcc-cp Rat: Model of Obesity, Non-insulin-dependent Diabetes, and Congestive Heart Failure , 1990 .
[64] Ulrich Mansmann,et al. GlobalANCOVA: exploration and assessment of gene group effects , 2008, Bioinform..
[65] R. Young,et al. Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays , 2004, Nature Genetics.
[66] Martin Vingron,et al. PASTAA: identifying transcription factors associated with sets of co-regulated genes , 2008, Bioinform..
[67] T. Speed,et al. Summaries of Affymetrix GeneChip probe level data. , 2003, Nucleic acids research.
[68] Serge Batalov,et al. Genomewide Association Analysis in Diverse Inbred Mice: Power and Population Structure , 2007, Genetics.
[69] T. Brody,et al. On the power of experimental designs for the detection of linkage between marker loci and quantitative loci in crosses between inbred lines , 2004, Theoretical and Applied Genetics.
[70] Hideo Negishi,et al. IRF-7 is the master regulator of type-I interferon-dependent immune responses , 2005, Nature.
[71] J. Zhu,et al. An integrative genomics approach to the reconstruction of gene networks in segregating populations , 2004, Cytogenetic and Genome Research.
[72] E. Petretto,et al. Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease , 2005, Nature Genetics.
[73] Claude Lenfant,et al. Definition of Metabolic Syndrome: Report of the National Heart, Lung, and Blood Institute/American Heart Association Conference on Scientific Issues Related to Definition , 2004, Arteriosclerosis, thrombosis, and vascular biology.
[74] E E Schadt,et al. Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits , 2005, Nature Genetics.
[75] Alan Salama,et al. Jund is a determinant of macrophage activation and is associated with glomerulonephritis susceptibility , 2008, Nature Genetics.
[76] M. Spence,et al. Mapping of quantitative trait loci for blood pressure and cardiac mass in the rat by genome scanning of recombinant inbred strains. , 1995, The Journal of clinical investigation.
[77] P. O’Reilly,et al. Genome-wide association study identifies eight loci associated with blood pressure , 2009, Nature Genetics.
[78] Francis S. Collins,et al. Variations on a Theme: Cataloging Human DNA Sequence Variation , 1997, Science.
[79] C. Coban,et al. Interferon-α induction through Toll-like receptors involves a direct interaction of IRF7 with MyD88 and TRAF6 , 2004, Nature Immunology.
[80] P. Khatri,et al. Global functional profiling of gene expression. , 2003, Genomics.
[81] Edwin Cuppen,et al. Progress and prospects in rat genetics: a community view , 2008, Nature Genetics.
[82] Alexandre V. Morozov,et al. Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE , 2006, ISMB.
[83] Mrinal Kalakrishnan,et al. An Integrative Network Approach to Map the Transcriptome to the Phenome , 2008, RECOMB.
[84] Z. Zeng,et al. Multiple interval mapping for quantitative trait loci. , 1999, Genetics.
[85] D. F. Morrison,et al. Multivariate Statistical Methods , 1968 .
[86] David N Arnosti,et al. Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? , 2005, Journal of cellular biochemistry.
[87] L. Tsui,et al. Erratum: Identification of the Cystic Fibrosis Gene: Genetic Analysis , 1989, Science.
[88] J. Lamb,et al. Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes , 2006, Journal of neurochemistry.
[89] D. Lockhart,et al. Expression monitoring by hybridization to high-density oligonucleotide arrays , 1996, Nature Biotechnology.
[90] M. Leite,et al. Nucleoplasmic Calcium Is Required for Cell Proliferation* , 2007, Journal of Biological Chemistry.
[91] E. Segal,et al. Predicting expression patterns from regulatory sequence in Drosophila segmentation , 2008, Nature.
[92] Serge Batalov,et al. Gene Set Enrichment in eQTL Data Identifies Novel Annotations and Pathway Regulators , 2008, PLoS genetics.
[93] Yan D. Zhao. Sample size estimation for the van Elteren test—a stratified Wilcoxon–Mann–Whitney test , 2006, Statistics in medicine.
[94] John D. Storey,et al. Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[95] Timothy L. Bailey,et al. Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data , 2010, BMC Bioinformatics.
[96] N. Samani,et al. Successful isolation of a rat chromosome 1 blood pressure quantitative trait locus in reciprocal congenic strains. , 1998, Hypertension.
[97] Korbinian Strimmer,et al. BMC Bioinformatics BioMed Central Methodology article A general modular framework for gene set enrichment analysis , 2009 .
[98] S. P. Fodor,et al. Light-directed, spatially addressable parallel chemical synthesis. , 1991, Science.
[99] P. Park,et al. Discovering statistically significant pathways in expression profiling studies. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[100] R. Rao. Insulin Resistance in Spontaneously Hypertensive Rats: Difference in Interpretation Based on Insulin Infusion Rate or on Plasma Insulin in Glucose Clamp Studies , 1993, Diabetes.
[101] S. Horvath,et al. Evidence for anti-Burkitt tumour globulins in Burkitt tumour patients and healthy individuals. , 1967, British Journal of Cancer.
[102] E. Birney,et al. SNP and haplotype mapping for genetic analysis in the rat , 2008, Nature Genetics.
[103] P. Deloukas,et al. Common Regulatory Variation Impacts Gene Expression in a Cell Type–Dependent Manner , 2009, Science.
[104] H. Stefánsson,et al. Genetics of gene expression and its effect on disease , 2008, Nature.
[105] J. Castle,et al. An integrative genomics approach to infer causal associations between gene expression and disease , 2005, Nature Genetics.
[106] Weller Ji. Maximum likelihood techniques for the mapping and analysis of quantitative trait loci with the aid of genetic markers. , 1986 .
[107] J. Nap,et al. Genetical genomics: the added value from segregation. , 2001, Trends in genetics : TIG.
[108] N. Hübner,et al. Congenic substitution mapping excludes Sa as a candidate gene locus for a blood pressure quantitative trait locus on rat chromosome 1. , 1999, Hypertension.
[109] M. Mann,et al. A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. , 2009, Genome research.
[110] V. Roger,et al. Trends in prevalence and outcome of heart failure with preserved ejection fraction. , 2006, The New England journal of medicine.
[111] G. Peltz,et al. Identification of complement factor 5 as a susceptibility locus for experimental allergic asthma , 2000, Nature Immunology.
[112] A. Hess,et al. Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays , 2007, BMC Genomics.
[113] J. Flint,et al. Quantitative trait loci for cellular defects in glucose and fatty acid metabolism in hypertensive rats , 1997, Nature Genetics.
[114] R. Berne,et al. Effect of Epinephrine and Norepinephrine on Coronary Circulation , 1958, Circulation research.
[115] Alison Abbott,et al. Return of the rat , 2009, Nature.
[116] Dudley J Pennell,et al. Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass , 2008, Nature Genetics.
[117] K. Dolinski,et al. Use and misuse of the gene ontology annotations , 2008, Nature Reviews Genetics.
[118] V. Křen. Genetics of the polydactyly-luxate syndrome in the Norway rat, Rattus norvegicus. , 1975, Acta Universitatis Carolinae. Medica. Monographia.
[119] Ronald W. Davis,et al. Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.
[120] J. Pagano,et al. Regulation of the Transcriptional Activity of the IRF7 Promoter by a Pathway Independent of Interferon Signaling* , 2005, Journal of Biological Chemistry.
[121] Zhen Jiang,et al. Bioconductor Project Bioconductor Project Working Papers Year Paper Extensions to Gene Set Enrichment , 2013 .
[122] B. Efron. SIMULTANEOUS INFERENCE : WHEN SHOULD HYPOTHESIS TESTING PROBLEMS BE COMBINED? , 2008, 0803.3863.
[123] Anthony Ralston,et al. Mathematical Methods for Digital Computers, Volume II. , 1968 .
[124] Korbinian Strimmer,et al. A unified approach to false discovery rate estimation , 2008, BMC Bioinformatics.
[125] T. Kurtz,et al. Quantitative trait loci influencing cholesterol and phospholipid phenotypes map to chromosomes that contain genes regulating blood pressure in the spontaneously hypertensive rat. , 1996, The Journal of clinical investigation.
[126] M. Berger,et al. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors , 2009, Nature Protocols.
[127] C. Ting,et al. A genome-wide association study identifies new loci for ACE activity: potential implications for response to ACE inhibitor , 2010, The Pharmacogenomics Journal.
[128] S. Hunt,et al. Genome-Wide Associations of Gene Expression Variation in Humans , 2005, PLoS genetics.
[129] B. Falkner,et al. Insulin resistance in the conscious spontaneously hypertensive rat: euglycemic hyperinsulinemic clamp study. , 1993, Metabolism: clinical and experimental.
[130] M. Daly,et al. Genetic Mapping in Human Disease , 2008, Science.
[131] Juan M. Vaquerizas,et al. A census of human transcription factors: function, expression and evolution , 2009, Nature Reviews Genetics.
[132] Rachel B. Brem,et al. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors , 2003, Nature Genetics.
[133] H. Jacob,et al. Use of AFLP markers for gene mapping and QTL detection in the rat. , 1996, Genomics.
[134] M. Gerstein,et al. Annotating non-coding regions of the genome , 2010, Nature Reviews Genetics.
[135] A. E. Hoerl,et al. Ridge regression: biased estimation for nonorthogonal problems , 2000 .
[136] Martin Vingron,et al. Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions , 2008, PLoS Comput. Biol..
[137] Robert Gentleman,et al. Using GOstats to test gene lists for GO term association , 2007, Bioinform..
[138] K. Okamoto. Spontaneous hypertension; its pathogenesis and complications , 1972 .
[139] C. Mallows. Some Comments on Cp , 2000, Technometrics.
[140] Paul A Lyons,et al. Combining mouse congenic strains and microarray gene expression analyses to study a complex trait: the NOD model of type 1 diabetes. , 2002, Genome research.
[141] S. Leal. Genetics and Analysis of Quantitative Traits , 2001 .
[142] David J. Arenillas,et al. In Silico Detection of Sequence Variations Modifying Transcriptional Regulation , 2007, PLoS Comput. Biol..
[143] Terence P. Speed,et al. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias , 2003, Bioinform..
[144] C. Mackay,et al. Guidance of B cells by the orphan G protein-coupled receptor EBI2 shapes humoral immune responses. , 2009, Immunity.
[145] J. Todd,et al. Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes , 2009, Science.
[146] R. Stoughton,et al. Genetics of gene expression surveyed in maize, mouse and man , 2003, Nature.
[147] Ole Winther,et al. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update , 2007, Nucleic Acids Res..
[148] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[149] Kiyoko F. Aoki-Kinoshita,et al. From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..
[150] Leonid Kruglyak,et al. The road to genome-wide association studies , 2008, Nature Reviews Genetics.
[151] G. Schwarz. Estimating the Dimension of a Model , 1978 .
[152] Elizabeth M. Smigielski,et al. dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..
[153] E. Schiffrin,et al. Inflammation in hypertension , 2006, Current opinion in nephrology and hypertension.
[154] P. Rosenbaum. Model-Based Direct Adjustment , 1987 .
[155] R. Doerge,et al. Empirical threshold values for quantitative trait mapping. , 1994, Genetics.
[156] Robert W. Williams,et al. WebQTL - Web-based complex trait analysis , 2003, Neuroinformatics.
[157] W. Hays. Statistical theory. , 1968, Annual review of psychology.
[158] S. Horvath,et al. Variations in DNA elucidate molecular networks that cause disease , 2008, Nature.
[159] José Crossa,et al. Predicting Quantitative Traits With Regression Models for Dense Molecular Markers and Pedigree , 2009, Genetics.
[160] D. Eizirik,et al. The role of inflammation in insulitis and , 2009 .
[161] J. Cyster,et al. EBV induced molecule-2 mediates B cell segregation between outer and center follicle , 2009, Nature.
[162] M. Kendall. Statistical Methods for Research Workers , 1937, Nature.
[163] Rappold,et al. Human Molecular Genetics , 1996, Nature Medicine.
[164] L. Liang,et al. Mapping complex disease traits with global gene expression , 2009, Nature Reviews Genetics.
[165] David BotsteinS’B. Mapping Mendelian Factors Underlying Quantitative Traits Using RFLP Linkage Maps , 2002 .
[166] Alexander E. Kel,et al. TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes , 2005, Nucleic Acids Res..
[167] E. Schadt. Molecular networks as sensors and drivers of common human diseases , 2009, Nature.
[168] V. Ingram,et al. A Specific Chemical Difference Between the Globins of Normal Human and Sickle-Cell Anæmia Hæmoglobin , 1956, Nature.
[169] Anirvan M. Sengupta,et al. A biophysical approach to transcription factor binding site discovery. , 2003, Genome research.