Disentangling molecular relationships with a causal inference test
Tóm tắt
Từ khóa
Tài liệu tham khảo
Chen LS, Emmert-Streib F, Storey JD: Harnessing naturally randomized transcription to infer regulatory relationships among genes. Genome Biol. 2007, 8 (10): R219-10.1186/gb-2007-8-10-r219.
Chen Y, Zhu J, Lum PY, Yang X, Pinto S, MacNeil DJ, Zhang C, Lamb J, Edwards S, Sieberts SK, et al: Variations in DNA elucidate molecular networks that cause disease. Nature. 2008, 452 (7186): 429-435. 10.1038/nature06757.
Davey Smith G, Ebrahim S: 'Mendelian randomization': can genetic epidemiology contribute to understanding environmental determinants of disease?. Int J Epidemiol. 2003, 32 (1): 1-22. 10.1093/ije/dyg070.
Didelez V, Sheehan N: Mendelian randomization as an instrumental variable approach to causal inference. Stat Methods Med Res. 2007, 16 (4): 309-330. 10.1177/0962280206077743.
Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, Helgason A, Walters GB, Gunnarsdottir S, et al: Genetics of gene expression and its effect on disease. Nature. 2008, 452 (7186): 423-428. 10.1038/nature06758.
Kulp DC, Jagalur M: Causal inference of regulator-target pairs by gene mapping of expression phenotypes. BMC Genomics. 2006, 7: 125-10.1186/1471-2164-7-125.
Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D, Sieberts SK, Monks S, Reitman M, Zhang C, et al: An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet. 2005, 37 (7): 710-717. 10.1038/ng1589.
Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, et al: Genetics of gene expression surveyed in maize, mouse and man. Nature. 2003, 422 (6929): 297-302. 10.1038/nature01434.
Zhu J, Lum PY, Lamb J, GuhaThakurta D, Edwards SW, Thieringer R, Berger JP, Wu MS, Thompson J, Sachs AB, et al: An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenet Genome Res. 2004, 105 (2–4): 363-374. 10.1159/000078209.
Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE: Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet. 2008, 40 (7): 854-861. 10.1038/ng.167.
Lawlor DA, Harbord RM, Sterne JA, Timpson N, Davey Smith G: Mendelian randomization: using genes as instruments for making causal inferences in epidemiology. Stat Med. 2008, 27 (8): 1133-1163. 10.1002/sim.3034.
Nitsch D, Molokhia M, Smeeth L, DeStavola BL, Whittaker JC, Leon DA: Limits to causal inference based on Mendelian randomization: a comparison with randomized controlled trials. Am J Epidemiol. 2006, 163 (5): 397-403. 10.1093/aje/kwj062.
Li R, Tsaih SW, Shockley K, Stylianou IM, Wergedal J, Paigen B, Churchill GA: Structural model analysis of multiple quantitative traits. PLoS Genet. 2006, 2 (7): e114-10.1371/journal.pgen.0020114.
Li H, Lu L, Manly KF, Chesler EJ, Bao L, Wang J, Zhou M, Williams RW, Cui Y: Inferring gene transcriptional modulatory relations: a genetical genomics approach. Hum Mol Genet. 2005, 14 (9): 1119-1125. 10.1093/hmg/ddi124.
Zhang B, Horvath S: A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005, 4: Article17.
Cassella G, Berger RL: Statistical Inference. 2002, Pacific Grove, CA: Duxbury
Broman KW, Wu H, Sen S, Churchill GA: R/qtl: QTL mapping in experimental crosses. Bioinformatics. 2003, 19 (7): 889-890. 10.1093/bioinformatics/btg112.
Bottcher SG, Dethlefsen C: deal: A package for learning Bayesian networks. Journal of Statistical Software. 2003, 8: 1-40.
Brem RB, Kruglyak L: The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci USA. 2005, 102 (5): 1572-1577. 10.1073/pnas.0408709102.
von Rohr P, Friberg MT, Kadarmideen HN: Prediction of transcription factor binding sites using genetical genomics methods. J Bioinform Comput Biol. 2007, 5 (3): 773-793. 10.1142/S0219720007002680.
Kang HM, Ye C, Eskin E: Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics. 2008, 180 (4): 1909-1925. 10.1534/genetics.108.094201.
Leek JT, Storey JD: A general framework for multiple testing dependence. Proc Natl Acad Sci USA. 2008, 105 (48): 18718-18723. 10.1073/pnas.0808709105.