Inferring gene transcriptional modulatory relations: A genetical genomics approach

Human Molecular Genetics

Volumn 14, Issue 9, 2005, Pages 1119-1125

  Li, Hongqiang ^a   Lu, Lu ^a   Manly, Kenneth F ^a   Chesler, Elissa J ^a   Bao, Lei ^a   Wang, Jintao ^a   Zhou, Mi ^a   Williams, Robert W ^a   Cui, Yan ^a  

^a UNIVERSITY OF TENNESSEE HEALTH SCIENCE CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSCRIPTOME;

ARTICLE; BAYES THEOREM; DNA FINGERPRINTING; DNA MICROARRAY; GENETIC POLYMORPHISM; GENETIC TRANSCRIPTION; GENOMICS; MESSENGER RNA SYNTHESIS; MOUSE; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; VIRUS STRAIN;

ALGORITHMS; ANIMALS; BAYES THEOREM; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; CROSSES, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENE TARGETING; GENETIC MARKERS; GENETICS, POPULATION; GENOMICS; MALE; MICE; MICE, INBRED C57BL; MICE, INBRED DBA; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE; TRANSCRIPTION, GENETIC;

EID: 18144399354     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/ddi124     Document Type: Article

References (52)

1. Jansen, R.C. and Nap, J.P. (2001) Genetical genomics: the added value from segregation. Trends Genet., 17, 388-391.
2. Liu, H.C., Cheng, H.H., Tirunagaru, V., Sofer, L. and Burnside, J (2001) A strategy to identify positional candidate genes conferring Marek's disease resistance by integrating DNA microarrays and genetic mapping. Anim. Genet., 32, 351-359.
3. Brem, R.B., Yvert, G., Clinton, R. and Kruglyak, L. (2002) Genetic dissection of transcriptional regulation in budding yeast. Science, 296, 752-755.
4. Eaves, I.A., Wicker, L.S., Ghandour, G., Lyons, P.A., Peterson, L.B., Todd, J.A. and Glynne, R.J. (2002) Combining mouse congenic strains and microarray gene expression analyses to study a complex trait: the NOD model of type 1 diabetes. Genome Res., 12, 232-243.
5. Manly, K.F., Wang, J., Shou, S., Qu, Y., Chesler, E., Lu, L., Hsu, H.C., Mountz J.D., Threadgill, D.W. and Williams, R.W. (2002) QTL mapping with microarray expression data. 16th International Mouse Genome Conference, San Antonio, TX.
6. Wayne, M.L. and McIntyre, L.M. (2002) Combining mapping and arraying: an approach to candidate gene identification. Proc. Natl Acad. Sci. USA, 99, 14903-14906.
7. Williams, R.W., Manly, K.F., Shou, S., Chesler, E., Hsu, H.C., Mountz, J.D., Wang, J., Threadgill, D.W. and Lu, L. (2002) Massively parallel complex trait analysis of transcriptional activity in mouse brain. 16th International Mouse Genome Conference, San Antonio, TX.
8. Schadt, E.E., Monks, S.A., Drake, T.A., Lusis, A.J., Che, N., Colinayo, V., Ruff, T.G., Milligan, S.B., Lamb, J.R., Cavet, G. et al. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature, 422, 297-302.
9. Chesler, E.J., Lu, L., Wang, J., Williams, R.W. and Manly, K.F. (2004) WebQTL: rapid exploratory analysis of gene expression and genetic networks for brain and behavior. Nat. Neurosci., 7, 485-486.
10. Morley, M., Molony, C.M., Weber, T.M., Devlin, J.L., Ewens, K.G., Spielman, R.S. and Cheung, V.G. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature, 430, 743-747.
11. Chesler, E.J., Lu, L., Shou, S., Qu, Y., Gu, J., Wang, J., Hsu, H.C., Mountz, J.D., Baldwin, N.E., Langston, M.A. et al. (2005) Complex trait analysis of gene expression reveals polygenic and pleiotropic networks that modulate nervous system function. Nat. Genet., 37, 233-242.
12. Bystrykh, L., Weersing, E., Dontje, B., Sutton, S., Pletcher, M.T., Wiltshire, T., Su, A.I., Vellenga, E., Wang, J., Manly, K.F. et al. (2005) Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Nat. Genet., 37, 225-232.
13. Hubner, N., Wallace, C.A., Zimdahl, H., Petretto, E., Schulz, H., Maciver, F., Mueller, M., Hummel, O., Monti, J., Zidek, V. et al. (2005) Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat. Genet., 37, 243-253.
14. Freidman, N., Linial, M., Nachman, I. and Peer, D. (2000) Using Bayesian networks to analyze expression data. J. Comput. Biol., 7, 601-620.
15. Peer, D., Regev, A., Elidan, G. and Friedman, N. (2001) Inferring subnetworks from perturbed expression profiles. Bioinformatics, 17, S215-S224.
16. Hartemink, A.J., Gifford, D.K., Jaakkola, T.S. and Young, R.A. (2001) Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pac. Symp. Biocomput., 422-433.
17. Spirtes, P., Glymour, C., Scheines, R., Kauffman, S., Aimale, V. and Wimberly, F. (2001) Constructing Bayesian network models of gene expression networks from microarray data. Proceedings of the Atlantic Symposium on Computational Biology, Genome Information Systems and Technology.
18. Yoo, C., Thorsson, V. and Cooper, G.F. (2002) Discovery of causal relationships in a gene-regulation pathway from a mixture of experimental and observational DNA microarray data. Pac. Symp. Biocomput., 486-509.
19. Imoto, S., Goto, T. and Miyano, S. (2002) Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression. Pac. Symp. Biocomput., 175-186.
20. Imoto, S., Kim, S., Goto, T., Miyano, S., Aburatani, S., Tashiro, K. and Kuhara, S. (2003) Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. J. Bioinform. Comput. Biol., 1, 231-252.
21. Chu, T., Glymour, C., Scheines, R. and Spirtes, P. (2003) A statistical problem for inference to regulatory structure from associations of gene expression measurement with microarrays. Bioinformatics, 19, 1147-1152.
22. Husmeier, D. (2003) Reverse engineering of genetic networks with Bayesian networks. Biochem. Soc. Trans., 31, 1516-1518.
23. Tamada, Y., Kim, S., Bannai, H., Imoto, S., Tashiro, K., Kuhara, S. and Miyano, S. (2003) Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics, 19, 227-236.
24. Friedman, N. (2003) Probabilistic models for identifying regulation networks. Bioinformatics, 19, II57.
25. Friedman, N. (2004) Inferring cellular networks using probabilistic graphical models. Science, 303, 799-805.
26. Li, Z. and Chan, C. (2004) Inferring pathways and networks with a Bayesian framework. FASEB J., 18, 746-748.
27. Lu, X., Wang, X., Huang, Y., Hu, W., Gao, G., Li, Y. and Zhang, X., (2004) On some choices in Bayesian network learning for reconstructing regulatory networks. Proceedings of RECOMB04, 126-127.
28. Xia, Y., Yu, H., Jansen, R., Seringhaus, M., Baxter, S., Greenbaum, D., Zhao, H. and Gerstein, M. (2004) Analyzing cellular biochemistry in terms of molecular networks. Annu. Rev. Biochem., 73, 1051-1087.
29. Chickering, D. (1996) Learning Bayesian network is NP-complete. In Fisher, D. and Lenz, H. (eds), Learning from Data: Artificial Intelligence and Statistics V. Springer-Verlag, Heidelberg, pp. 121-130.
30. Peirce, J.L., Lu, L., Gu, J., Silver, L.M. and Williams, R.W. (2004) A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genet., 5, 7.
31. Plomin, R., McClearn, G.E., Gora-Maslak, G. and Neiderhiser, J.M. (1991) Use of recombinant inbred strains to detect quantitative trait loci associated with behavior. Behav. Genet., 21, 99-116.
32. Wang, J., Williams, R.W. and Manly, K.F. (2003) WebQTL: web-based complex trait analysis. Neuroinformatics, 1, 299-308.
33. Chesler, E.J., Wang, J., Lu, L., Qu, Y., Manly, K.F. and Williams, R.W. (2003) Genetic correlates of gene expression in recombinant inbred strains. Neuroinformatics., 1, 343-357.
34. Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2005) NCBI reference sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33, D501-D504.
35. Kerlavage, A., Bonazzi, V., di Tommaso, M., Lawrence, C., Li, P., Mayberry, F., Mural, R., Nodell, M., Yandell, M., Zhang, J. and Thomas, P. (2002) The celera discovery system. Nucleic Acids Res., 30, 129-136.
36. Kent, W.J. (2002) BLAT - the bLAST-like alignment tool, Genome Res., 12, 656-664.
37. Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A.E., Kel-Margoulis, O.V. et al. (2003) TRANSFAC®: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
38. Kel, A.E, Gossling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O.V. and Wingender, E. (2003) MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res., 31, 3576-3579.
39. Imoto, S., Higuchi, T., Goto, T., Tashiro, K., Kuhara, S. and Miyano, S. (2004) Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. J. Bioinform. Comput. Biol., 2, 77-98.
40. Zhu, J., Lum, P.Y., Lamb, J., GuhaThakurta, D., Edwards, S.W., Thieringer, R., Berger, J.P., Wu, M.S., Thompson, J., Sachs, A.B. and Schadt, E.E. (2004) An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenet. Genome Res., 105, 363-374.
41. Zou, M. and Conzen, S.D. (2005) A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data. Bioinformatics, 21, 71-79.
42. The Gene Ontology Consortium. (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25-29.
43. Mewes, H.W., Frishman, D., Güldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., Morgenstern, B., Münsterkoetter, M., Rudd, S. and Weil, B. (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res., 30, 31-34.
44. Kanehisa, M. and Goto, S. (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
45. Haley, C.S. and Knott, S.A. (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity, 69, 315-324.
46. Pearl, J. (1988) Probabilistic Reasoning in Intelligent Systems. Morgan Kaufmann Publishers, CA.
47. Pearl, J. (2000) Causality: Models, Reasoning, and Inference. Cambridge University Press, Cambridge UK.
48. Heckerman, D. (1999) A tutorial on learning with Bayesian networks. In Jordan, M. (ed.) Learning in Graphical Models. MIT Press, Cambridge, MA.
49. Buntine, W. (1991) Theory refinement on Bayesian networks. Proceedings of the Seventh Annual Conference on Uncertainty in Artificial Intelligence, Morgan Kaufman Publishers, CA, pp. 52-60.
50. Kamada, T. and Kawai, S. (1989) An algorithm for drawing general undirected graphs. Inform. Process. Lett., 31, 7-15.
51. Batagelj, V. and Mrvar, A. (2003) Pajek - analysis and visualization of large networks. In Jünger, M. and Mutzel, P. (eds), Graph Drawing Software. Springer, Berlin, pp. 77-103.
52. Batagelj, V. and Mrvar, A. (1998) Pajek - program for large network analysis. Connections, 21, 47-57.