CAPE: An R Package for Combined Analysis of Pleiotropy and Epistasis

PLoS Computational Biology

Volumn 9, Issue 10, 2013, Pages

  Tyler, Anna L ^a   Lu, Wei ^a,b   Hendrick, Justin J ^a   Philip, Vivek M ^a   Carter, Gregory W ^a  

^a JACKSON LABORATORY   (United States)

^b Duke University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX NETWORKS; POPULATION STATISTICS;

BIOLOGICAL SIGNIFICANCE; COMBINED ANALYSIS; COMPLEX TRAITS; GENE-GENE INTERACTION; GENETIC ARCHITECTURE; GENETIC COMPLEXITY; GENETIC STUDIES; GENETIC VARIANTS; HUMAN ORGANISMS; MODEL ORGANISMS;

GENES;

ARTICLE; BACKCROSSING; BIOINFORMATICS; BIOLOGICAL ACTIVITY; DATA ANALYSIS SOFTWARE; EPISTASIS; GENE INTERACTION; GENE REPRESSION; PHENOTYPIC VARIATION; PLEIOTROPY; QUANTITATIVE TRAIT;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; DIABETES MELLITUS, TYPE 2; DISEASE MODELS, ANIMAL; EPISTASIS, GENETIC; GENETIC PLEIOTROPY; LINEAR MODELS; MICE; MODELS, GENETIC; OBESITY; SOFTWARE;

EID: 84887290646     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003270     Document Type: Article

References (13)

1. Reifsnyder PC, (2000) Maternal Environment and Genotype Interact to Establish Diabesity in Mice. Genome Research 10: 1568-1578.
2. Broman KW, Wu H, Sen S, Churchill GA, (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889-890.
3. Carter GW, Hays M, Sherman A, Galitski T, (2012) Use of pleiotropy to model genetic interactions in a population. PLoS Genetics 8: e1003010.
4. Holm S, (1979) A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics 6: 65-70.
5. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B (Methodological) 57: 289-300.
6. Liao JG, Lin Y, Selvanayagam ZE, Shih WJ, (2004) A mixture model for estimating the local false discovery rate in DNA microarray analysis. Bioinformatics 20: 2694-2701.
7. Permutt MA, Wasson J, Cox N, (2005) Genetic epidemiology of diabetes. The Journal of Clinical Investigation 115: 1431-1439.
8. Burcelin R, Crivelli V, Dacosta A, Roy-Tirelli A, Thorens B, (2002) Heterogeneous metabolic adaptation of C57BL/6J mice to high-fat diet. American Journal of Physiology Endocrinology and Metabolism 282: E834-42.
9. Carter GW, (2013) Inferring gene function and network organization in Drosophila signaling by combined analysis of pleiotropy and epistasis. G3: Genes{pipe}Genomes{pipe}Genetics 3: 807-814.
10. Yandell BS, Mehta T, Banerjee S, Shriner D, Venkataraman R, et al. (2007) R/qtlbim: QTL with Bayesian interval mapping in experimental crosses. Bioinformatics 23: 641-643.
11. Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, et al. (2004) The collaborative cross, a community resource for the genetic analysis of complex traits. Nature Genetics 36: 1133-1137.
12. Svenson KL, Gatti DM, Valdar W, Welsh CE, Cheng R, et al. (2012) High-resolution genetic mapping using the mouse diversity outbred population. Genetics 190: 437-447.
13. Talbot CJ, Nicod A, Cherny SS, Fulker DW, Collins AC, et al. (1999) High-resolution mapping of quantitative trait loci in outbred mice. Nature Genetics 21: 305-308.