Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations

PLoS Computational Biology

Volumn 3, Issue 4, 2007, Pages 692-703

  Zhu, Jun ^a   Wiener, Matthew C ^b   Zhang, Chunsheng ^a   Fridman, Arthur ^b   Minch, Eric ^b   Lum, Pek Y ^a   Sachs, Jeffrey R ^b   Schadt, Eric E ^a  

^a ROSETTA INPHARMATICS   (United States)

^b MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DESIGN OF EXPERIMENTS; GENE EXPRESSION; POPULATION STATISTICS;

ENVIRONMENTAL FACTORS; EXPRESSION DATA; GENE EXPRESSION DATA; GENETIC FACTORS; HUMAN DISEASE; MULTIPLE PERTURBATIONS; NETWORK RECONSTRUCTION; POWER; PREDICTIVE NETWORK MODEL; RECONSTRUCTION ACCURACY;

BAYESIAN NETWORKS;

ARTICLE; BAYES THEOREM; CAUSAL ATTRIBUTION; GENE EXPRESSION; GENE INTERACTION; GENOMICS; GENOTYPE; HERITABILITY; PHENOTYPE; SIMULATION; ANIMAL; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; GENETICS; METABOLISM; METHODOLOGY; MOUSE; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; SIGNAL TRANSDUCTION;

PROTEOME;

ANIMALS; COMPUTER SIMULATION; DNA MUTATIONAL ANALYSIS; GENE EXPRESSION PROFILING; GENETIC VARIATION; GENOTYPE; MICE; MODELS, BIOLOGICAL; MULTIGENE FAMILY; PROTEOME; SIGNAL TRANSDUCTION;

EID: 34247556038     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030069     Document Type: Article

References (42)

1. Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, et al. (2005) An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet 37: 710-717.
2. Pearl J (1988) Probabilistic reasoning in intelligent systems: Networks of plausible inference. San Mateo (California): Morgan Kaufmann Publishers. p. xix. 552 p.
3. Pe'er D, Regev A, Elidan G, Friedman N (2001) Inferring subnetworks from perturbed expression profiles. Bioinformatics 17 (Supplement 1): S215-S224.
4. Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP (2005) Causal protein-signaling networks derived from multiparameter single-cell data. Science 308: 523-529.
5. Zhu J, Lum PY, Lamb J, GuhaThakurta D, Edwards SW, et al. (2004) An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenet Genome Res 105: 363-374.
6. Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
7. Monks SA, Leonardson A, Zhu H, Cundiff P, Pietrusiak P, et al. (2004) Genetic inheritance of gene expression in human cell lines. Am J Hum Genet 75: 1094-1105.
8. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, et al. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature 430: 743-747.
9. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, et al. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
10. Doss S, Schadt EE, Drake TA, Lusis AJ (2005) Cis-acting expression quantitative trait loci in mice. Genome Res 15: 681-691.
11. Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
12. Lum PY, Chen Y, Zhu J, Lamb J, Melmed S, et al. (2006) Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes. J Neurochem 97 (Supplement 1): 50-62.
13. Cervino AC, Li G, Edwards S, Zhu J, Laurie C, et al. (2005) Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels. Genomics 86: 505-517.
14. Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, et al. (2002) A genomic regulatory network for development. Science 295: 1669-1678.
15. Gardner TS, di Bernardo D, Lorenz D, Collins JJ (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105.
16. Zhu J, Chen Y, Lum PY, Davis RC, Lusis AJ, et al. (2005) Modeling gene perturbations in genome-tagged mice. Proceedings of the 2005 American Statistical Association Meeting, Biometics Section [CD-ROM]; 28-30 October 2005; Boston, Massachusetts, United States. Alexandria (Virginia): American Statistical Association. pp. 485-492.
17. Marcotte EM, Xenarios I, Eisenberg D (2001) Mining literature for protein-protein interactions. Bioinformatics 17: 359-363.
18. Xenarios I, Fernandez E, Salwinski L, Duan XJ, Thompson MJ, et al. (2001) DIP: The Database of Interacting Proteins: 2001 update. Nucleic Acids Res 29: 239-241.
19. Kulp DC, Jagalur M (2006) Causal inference of regulator-target pairs by gene mapping of expression phenotypes. BMC Genomics 7: 125.
20. Li R, Tsaih SW, Shockley K, Stylianou IM, Wergedal J, et al. (2006) Structural model analysis of multiple quantitative traits. PLoS Genet 2: e114.
21. Jansen RC, Nap JP (2001) Genetical genomics: The added value from segregation. Trends Genet 17: 388-391.
22. Smith VA, Jarvis ED, Hartemink AJ (2002) Evaluating functional network inference using simulations of complex biological systems. Bioinformatics 18 (Supplement 1): S216-S224.
23. Yu J, Smith VA, Wang PP, Hartemink AJ, Jarvis ED (2004) Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics 20: 3594-3603.
24. Van den Bulcke T, Van Leemput K, Naudts B, van Remortel P, Ma H, et al. (2006) SynTReN: A generator of synthetic gene expression data for design and analysis of structure learning algorithms. BMC Bioinformatics 7: 43.
25. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, et al. (2005) Uncovering regulatory pathways that affect hematopoietic stem cell function using "genetical genomics." Nat Genet 37: 225-232.
26. Chesler EJ, Lu L, Shou S, Qu Y, Gu J, et al. (2005) Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 37: 233-242.
27. Mehrabian M, Allayee H, Stockton J, Lum PY, Drake TA, et al. (2005) Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits. Nat Genet 37: 1224-1233.
28. Storey JD, Akey JM, Kruglyak L (2005) Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biol 3: e267.
29. Ronald J, Brem RB, Whittle J, Kruglyak L (2005) Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet 1: e25.
30. Ong IM, Glasner JD, Page D (2002) Modelling regulatory pathways in E. coli from time series expression profiles. Bioinformatics 18 (Supplement 1): S241-S248.
31. Rabiner LR (1989) A tutorial on Hidden Markov Models and selected applications in speech recognition. Proceedings of the 77th Meeting of the Institute of Electrical and Electronics Engineers, 15-18 May 1989; San Diego, California, United States. IEEE 77: 257-286.
32. Basten CA, Weir BS, Zeng ZB (1999) QTL Cartographer: A reference manual and tutorial for QTL mapping. Raleigh (North Carolina): Department of Statistics, North Carolina State University.
33. Wang S, Yehya N, Schadt EE, Wang H, Drake TA, et al. (2006) Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genet 2: e15.
34. Zhang LV, King OD, Wong SL, Goldberg DS, Tong AH, et al. (2005) Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J Biol 4: 6.
35. Barabasi AL, Albert R (1999) Emergence of scaling in random networks. Science 286: 509-512.
36. Cockerham CC (1954) An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present. Genetics 39: 859-882.
37. Kholodenko BN, Demin OV, Moehren G, Hoek JB (1999) Quantification of short term signaling by the epidermal growth factor receptor. J Biol Chem 274: 30169-30181.
38. He YD, Dai H, Schadt EE, Cavet G, Edwards SW, et al. (2003) Microarray standard data set and figures of merit for comparing data processing methods and experiment designs. Bioinformatics 19: 956-965.
39. Madigan D, York J (1995) Bayesian graphical models for discrete data. Intl Stat Rev 63: 215-232.
40. Schwarz G (1978) Estimating the dimension of a model. Ann Stat 6: 461-464.
41. Kruglyak L, Lander ES (1995) A nonparametric approach for mapping quantitative trait loci. Genetics 139: 1421-1428.
42. Jiang C, Zeng ZB (1995) Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140: 1111-1127.