Integrating Global Gene Expression Analysis and Genetics

Abelson, 2005, Sequence variants in SLITRK1 are associated with Tourette's syndrome, Science, 310, 317, 10.1126/science.1116502 Aitman, 1999, Identification of Cd36 (Fat) as an insulin‐resistance gene causing defective fatty acid and glucose metabolism in hypertensive rats, Nat. Genet., 21, 76, 10.1038/5013 Alwine, 1977, Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl‐paper and hybridization with DNA probes, Proc. Natl. Acad. Sci. USA, 74, 5350, 10.1073/pnas.74.12.5350 Ashburner, 2000, Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium, Nat. Genet., 25, 25, 10.1038/75556 Barabasi, 1999, Emergence of scaling in random networks, Science, 286, 509, 10.1126/science.286.5439.509 Brem, 2005, The landscape of genetic complexity across 5,700 gene expression traits in yeast, Proc. Natl. Acad. Sci. USA, 102, 1572, 10.1073/pnas.0408709102 Brem, 2002, Genetic dissection of transcriptional regulation in budding yeast, Science, 296, 752, 10.1126/science.1069516 Brem, 2005, Genetic interactions between polymorphisms that affect gene expression in yeast, Nature, 436, 701, 10.1038/nature03865 Brenner, 2000, Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays, Nat. Biotechnol., 18, 630, 10.1038/76469 Butte, 2002, The use and analysis of microarray data, Nat. Rev. Drug Discov., 1, 951, 10.1038/nrd961 Cheung, 2005, Mapping determinants of human gene expression by regional and genome‐wide association, Nature, 437, 1365, 10.1038/nature04244 Clop, 2006, A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep, Nat. Genet., 38, 813, 10.1038/ng1810 Dalma‐Weiszhausz, 2006, The affymetrix GeneChip platform: An overview, Methods Enzymol., 410, 3, 10.1016/S0076-6879(06)10001-4 Darvasi, 1998, Experimental strategies for the genetic dissection of complex traits in animal models, Nat. Genet., 18, 19, 10.1038/ng0198-19 Dennis, 2003, DAVID: Database for annotation, visualization, and integrated discovery, Genome Biol., 4, P3, 10.1186/gb-2003-4-5-p3 DeRisi, 1996, Use of a cDNA microarray to analyse gene expression patterns in human cancer, Nat. Genet., 14, 457, 10.1038/ng1296-457 Diament, 2004, Multiple linked mouse chromosome 7 loci influence body fat mass, Int. J. Obes. Relat. Metab. Disord., 28, 199, 10.1038/sj.ijo.0802516 Doerge, 2002, Mapping and analysis of quantitative trait loci in experimental populations, Nat. Rev. Genet., 3, 43, 10.1038/nrg703 Doss, 2005, Cis‐acting expression quantitative trait loci in mice, Genome Res., 15, 681, 10.1101/gr.3216905 Edderkaoui, 2006, Multiple genetic loci from CAST/EiJ chromosome 1 affect vBMD either positively or negatively in a C57BL/6J background, J. Bone Miner. Res., 21, 97, 10.1359/JBMR.051008 Ehrenreich, 2006, DNA microarray technology for the microbiologist: An overview, Appl. Microbiol. Biotechnol., 73, 255, 10.1007/s00253-006-0584-2 Falconer, 1996 Fan, 2006, Illumina universal bead arrays, Methods Enzymol., 410, 57, 10.1016/S0076-6879(06)10003-8 Flint, 2005, Strategies for mapping and cloning quantitative trait genes in rodents, Nat. Rev. Genet., 6, 271, 10.1038/nrg1576 Fodor, 1991, Light‐directed, spatially addressable parallel chemical synthesis, Science, 251, 767, 10.1126/science.1990438 Gargalovic, 2006, Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids, Proc. Natl. Acad. Sci. USA, 103, 12741, 10.1073/pnas.0605457103 Gentleman, 2004, Bioconductor: Open software development for computational biology and bioinformatics, Genome Biol., 5, R80, 10.1186/gb-2004-5-10-r80 Ghazalpour, 2005, Genomic analysis of metabolic pathway gene expression in mice, Genome Biol., 6, R59, 10.1186/gb-2005-6-7-r59 Ghazalpour, 2006, Integrating genetic and network analysis to characterize genes related to mouse weight, PLoS Genet., 2, e130, 10.1371/journal.pgen.0020130 Gibbs, 2004, Genome sequence of the Brown Norway rat yields insights into mammalian evolution, Nature, 428, 493, 10.1038/nature02426 Gunderson, 2004, Decoding randomly ordered DNA arrays, Genome Res., 14, 870, 10.1101/gr.2255804 Hager, 2006, Making and using spotted DNA microarrays in an academic core laboratory, Methods Enzymol., 410, 135, 10.1016/S0076-6879(06)10007-5 Hasegawa, 2004, Variations in the C3, C3a receptor, and C5 genes affect susceptibility to bronchial asthma, Hum. Genet., 115, 295, 10.1007/s00439-004-1157-z Hosack, 2003, Identifying biological themes within lists of genes with EASE, Genome Biol., 4, R70, 10.1186/gb-2003-4-10-r70 Hubank, 1994, Identifying differences in mRNA expression by representational difference analysis of cDNA, Nucleic Acids Res., 22, 5640, 10.1093/nar/22.25.5640 Jaluria, 2007, A perspective on microarrays: Current applications, pitfalls, and potential uses, Microb. Cell Fact., 6, 4, 10.1186/1475-2859-6-4 Jilka, 2003, Biology of the basic multicellular unit and the pathophysiology of osteoporosis, Med. Pediatr. Oncol., 41, 182, 10.1002/mpo.10334 Kapp, 2006, Discovery and validation of breast cancer subtypes, BMC Genomics, 7, 231, 10.1186/1471-2164-7-231 Karp, 2000, Identification of complement factor 5 as a susceptibility locus for experimental allergic asthma, Nat. Immunol., 1, 221, 10.1038/79759 Klein, 2004, Regulation of bone mass in mice by the lipoxygenase gene Alox15, Science, 303, 229, 10.1126/science.1090985 Koczan, 2006, Survey of microarray technologies suitable to elucidate transcriptional networks as exemplified by studying KRAB zinc finger gene families, Proteomics, 6, 4704, 10.1002/pmic.200600010 Konradi, 2005, Gene expression microarray studies in polygenic psychiatric disorders: Applications and data analysis, Brain Res. Brain Res. Rev., 50, 142, 10.1016/j.brainresrev.2005.05.004 Kuhn, 2004, A novel, high‐performance random array platform for quantitative gene expression profiling, Genome Res., 14, 2347, 10.1101/gr.2739104 Lamb, 2006, The connectivity map: Using gene‐expression signatures to connect small molecules, genes, and disease, Science, 313, 1929, 10.1126/science.1132939 Lander, 2001, Initial sequencing and analysis of the human genome, Nature, 409, 860, 10.1038/35057062 Lein, 2007, Genome‐wide atlas of gene expression in the adult mouse brain, Nature, 445, 168, 10.1038/nature05453 Liang, 1992, Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction, Science, 257, 967, 10.1126/science.1354393 Meng, 2007, Identification of Abcc6 as the major causal gene for dystrophic cardiac calcification in mice through integrative genomics, Proc. Natl. Acad. Sci. USA, 104, 4530, 10.1073/pnas.0607620104 Monks, 2004, Genetic inheritance of gene expression in human cell lines, Am. J. Hum. Genet., 75, 1094, 10.1086/426461 Mootha, 2003, PGC‐1alpha‐responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes, Nat. Genet., 34, 267, 10.1038/ng1180 Morley, 2004, Genetic analysis of genome‐wide variation in human gene expression, Nature, 430, 743, 10.1038/nature02797 Narayanan, 2007, Bioinformatics approaches to cancer gene discovery, Methods Mol, Biol., 360, 13 Perou, 2000, Molecular portraits of human breast tumours, Nature, 406, 747, 10.1038/35021093 Quackenbush, 2001, Computational analysis of microarray data, Nat. Rev. Genet., 2, 418, 10.1038/35076576 Rockman, 2006, Genetics of global gene expression, Nat. Rev. Genet., 7, 862, 10.1038/nrg1964 Schadt, 2003, Genetics of gene expression surveyed in maize, mouse and man, Nature, 422, 297, 10.1038/nature01434 Schadt, 2005, An integrative genomics approach to infer causal associations between gene expression and disease, Nat. Genet., 37, 710, 10.1038/ng1589 Schena, 1995, Quantitative monitoring of gene expression patterns with a complementary DNA microarray, Science, 270, 467, 10.1126/science.270.5235.467 Scheurle, 2000, Cancer gene discovery using digital differential display, Cancer Res., 60, 4037 Seeman, 2006, Bone quality—the material and structural basis of bone strength and fragility, N. Engl. J. Med., 354, 2250, 10.1056/NEJMra053077 Seo, 2004, Gene expression phenotypes of atherosclerosis, Arterioscler. Thromb. Vasc. Biol., 24, 1922, 10.1161/01.ATV.0000141358.65242.1f Shi, 2006, The MicroArray Quality Control (MAQC) project shows inter‐ and intraplatform reproducibility of gene expression measurements, Nat. Biotechnol., 24, 1151, 10.1038/nbt1239 Sorlie, 2001, Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications, Proc. Natl. Acad. Sci. USA, 98, 10869, 10.1073/pnas.191367098 Stoughton, 2005, Applications of DNA microarrays in biology, Annu. Rev. Biochem., 74, 53, 10.1146/annurev.biochem.74.082803.133212 Su, 2002, Large‐scale analysis of the human and mouse transcriptomes, Proc. Natl. Acad. Sci. USA, 99, 4465, 10.1073/pnas.012025199 Subramanian, 2005, Gene set enrichment analysis: A knowledge‐based approach for interpreting genome‐wide expression profiles, Proc. Natl. Acad. Sci USA, 102, 15545, 10.1073/pnas.0506580102 Tusher, 2001, Significance analysis of microarrays applied to the ionizing radiation response, Proc. Natl. Acad. Sci. USA, 98, 5116, 10.1073/pnas.091062498 van de Vijver, 2002, A gene‐expression signature as a predictor of survival in breast cancer, N. Engl. J. Med., 347, 1999, 10.1056/NEJMoa021967 van't Veer, 2002, Gene expression profiling predicts clinical outcome of breast cancer, Nature, 415, 530, 10.1038/415530a Velculescu, 1995, Serial analysis of gene expression, Science, 270, 484, 10.1126/science.270.5235.484 Venter, 2001, The sequence of the human genome, Science, 291, 1304, 10.1126/science.1058040 Walker, 2006, Databases of free expression, Mamm. Genome., 17, 1141, 10.1007/s00335-006-0043-5 Wang, 2006, Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity, PLoS Genet., 2, e15, 10.1371/journal.pgen.0020015 Waterston, 2002, Initial sequencing and comparative analysis of the mouse genome, Nature, 420, 520, 10.1038/nature01262 Wetsel, 1990, Deficiency of the murine fifth complement component (C5). A 2‐base pair gene deletion in a 5′‐exon, J. Biol. Chem., 265, 2435, 10.1016/S0021-9258(19)39817-5 Wit, 2004 Yang, 2006, Tissue‐specific expression and regulation of sexually dimorphic genes in mice, Genome Res., 16, 995, 10.1101/gr.5217506 Zhang, 2005, A general framework for weighted gene co‐expression network analysis, Stat. Appl. Genet. Mol. Biol., 4, 10.2202/1544-6115.1128