Causal inference of regulator-target pairs by gene mapping of expression phenotypes

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Kulp, David C ^a   Jagalur, Manjunatha ^a  

^a Biologically Inspired Neural and Dynamical Systems Laboratory   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; TRANS ACTING FACTOR; TRANSCRIPTION FACTOR;

ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE EXPRESSION PROFILING; GENE MAPPING; GENOTYPE; HOMEOSTASIS; LINKAGE ANALYSIS; PHENOTYPE; QUANTITATIVE TRAIT LOCUS MAPPING; SIMULATION; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; CROSSES, GENETIC; GENE EXPRESSION REGULATION; GENES, FUNGAL; GENES, REGULATOR; GENOTYPE; LIKELIHOOD FUNCTIONS; MICE; MICE, INBRED STRAINS; MODELS, GENETIC; PHENOTYPE; QUANTITATIVE TRAIT LOCI; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS;

EID: 33745483785     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-125     Document Type: Article

References (37)

1. Morley M, Molony C, Weber T, Devlin J, Ewens K, Spielman R, Cheung V: Genetic analysis of genome-wide variation in human gene expression. Nature 2004, 430(7001):743-7.
2. Schadt E, Monks S, Drake T, Lusis A, Che N, Colinayo V, Ruff T, Milligan S, Lamb J, Cavet G, Linsley P, Mao M, Stoughton R, Friend S: Genetics of gene expression surveyed in maize, mouse and man. Nature 2003, 422(6929):297-302.
3. Steinmetz L, Sinha H, Richards D, Spiegelman J, Oefner P, McCusker J, Davis R: Dissecting the architecture of a quantitative trait locus in yeast. Nature 2002, 416(6878):326-30.
4. Brem R, Yvert G, Clinton R, Kruglyak L: Genetic dissection of transcriptional regulation in budding yeast. Science 2002, 296(5568):752-5.
5. Brem R, Kruglyak L: The landscape of geneticcom plexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci USA 2005, 102(5):1572-7.
6. Chesler E, Lu L, Shou S, Qu Y, Gu J, Wang J, Hsu H, Mountz J, Baldwin N, Langston M, Threadgill D, Manly K, Williams R: Complex trait analysis of gene ex pression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 2005, 37(3):233-42.
7. Lander E, Botstein D: Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 1989, 121:185-99.
8. Yvert G, Brem R, Whittle J, Akey J, Foss E, Smith E, Mackelprang R, Kruglyak L: Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 2003, 35:57-64.
9. Spellman P, Sherlock G, Zhang M, Iyer V, Anders K, Eisen M, Brown P, Botstein D, Putcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9(12):3273-97.
10. Gasch A, Spellman P, Kao C, Carmel-Harell O, Eisen M, Storz G, Botstein D, Brown P: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 2000, 11(12):4241-57.
11. Hughes T, Marton M, Jones A, Roberts C, Stoughton R, Armour C, Bennett H, Coffey E, Dai H, He Y, Kidd M, King A, Meyer M, Slade D, Lum P, Stepaniants S, Shoemaker D, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend S: Functional discovery via a compendium of expression profiles. Cell 2000, 102:109-26.
12. Friedman N, Linial M, Nachman I, Pe'er D: Using Bayesian networks to analyze expression data. J Comput Biol 2000, 7(34):601-20.
13. Pearl J: Causality: models, reasoning, and inference Cambridge University Press; 2000.
14. Pe'er D, Regev A, Elidan G, Friedman N: Inferring subnetworks from perturbed expression profiles. Bioinformatics 2001, 17(Suppl 1):S215-24.
15. Hartemink A, Gifford D, Jaakkola T, Young R: Combining location and expression data for principled discovery of genetic regulatory network models. Pac Symp Biocomput 2002:437-49.
16. Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N: Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 2003, 34(2):166-76.
17. Friedman N, Murphy K. Russell S: Learning the structure of dynamic probabilistic networks. UAI 1998.
18. Zhu J, Lum P, Lamb J, GuhaThakurta D, Edwards S, Thieringer R, Berger J, Wu M, Thompson J, Sachs A, Schadt E: An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenet Genome Res 2004, 105(24):363-74.
19. Schadt E, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D, Sieberts S, Monks S, Reitman M, Zhang C, Lum P, Leonardson A, Thieringer R, Metzger J, Yang L, Castle J, Zhu H, Kash S, Drake T, Sachs A, Lusis A: An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet 2005, 37(7):710-7.
20. Li H, Lu L, Manly K, Chesler E, Bao L, Wang J, Zhou M, Williams R, Cui Y: Inferring gene transcriptional modulatory relations: a genetical genomics approach. Hum Mol Genet 2005, 14(9):1119-25.
21. Bing N, Hoeschele I: Genetical genomics analysis of a yeast segregant population for transcription network inference. Genetics 2005, 170(2):533-42.
22. Sen S, Churchill G: A statistical framework for quantitative trait mapping. Genetics 2001, 159:371-87.
23. Storey J, Akey J, Kruglyak L: Multiple Locus Linkage Analysis of Genomewide Expression in Yeast. PLoS Biology 2005, 3(8):.
24. Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J, Davis A, Dolinski K, Dwight S, Eppig J, Harris M, Hill D, Issel-Tarver L, Kasarskis A, Lewis S, Matese J, Richardson J, Ringwald M, Rubin G, Sherlock G: Gene ontology: tool for the unification of biology. Nat Genet 2000, 25:25-9.
25. Zhao Y, Sohn J, Warner J: Autoregulation in the biosynthesis of ribosomes. Mol Cell Biol 2003, 23(2):699-707.
26. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel A, Kel-Margoulis O, Kloos D, Land S, Lewicki-Potapov B, Michael H, Munch R, Renter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E: TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 2003, 31:374-8.
27. Cullin C, Baudin-Baillieu A, Guillemet E, Ozier-Kalogeropoulos O: Functional analysis of YCL09C: evidence for a role as the regulatory subunit of acetolactate synthase. Yeast 1996, 12(15):1511-8.
28. Pena J, Bjorkegren J, Tegner J: Growing Bayesian network models of gene networks from seed genes. Bioinformatics 2005, 21(Suppl 2):ii224-ii229.
29. Margolin A, Banerjee N, Nemenman I, Califano A: 2004 (http://www.menem.com/~ilya/digital_library/mypapers/ margolin-etal-b-04.pdf].
30. Tsamardinos I, Aliferis C, Statnikov A: Algorithms for Large Scale Markov Blanket Discovery. The 16th International FLAIRS Conference, St. Augustine, Florida 2003.
31. Cooper G, Herskovits E: A Bayesian method for the induction of probabilistic networks from data. Machine Learning 1992, 9(4):309-347.
32. Lynch M, Walsh B: Genetics and analysis of quantita tive traits Sunderland, Mass.: Sinauer; 1998. [97017666 Michael Lynch, Bruce Walsh. Includes bibliographical references (p. 891-[948]) and indexes.].
33. Jiang C, Zeng Z: Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 1995, 144)(3):1111-27.
34. Kastenmayer J, Ni L, Chu A, Kitchen L, Au W, Yang H, Carter C, Wheeler D, Davis R, Boeke J, Snyder M. Basrai M: Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Res 2006, 16(3):365-73.
35. Greenbaum D, Colangelo C, Williams K, Gerstein M: Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 2003, 4(9)-117.
36. Nachman I, Regev A, Friedman N: Inferring quantitative models of regulatory networks from expression data. Bioinformatics 2004, 20(Suppl 1):1248-1256.
37. Yu J, Smith A, Wang P, Hartemink A, Jarvis E: Using Bayesian Network Inference Algorithms to Recover Molecular Genetic Regulatory Networks. Third International Conference on Systems Biology 2002.