Association weight matrix: A network-based approach towards functional genome-wide association studies

Methods in Molecular Biology

Volumn 1019, Issue , 2013, Pages 437-447

  Reverter, Antonio ^a   Fortes, Marina R S ^b  

^a CSIRO   (Australia)

^b UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Complex multivariate phenotypes; Gene network; Genome wide association studies; Pathway analysis; Systems biology; Transcription factor analysis

Indexed keywords

ALGORITHM; ARTICLE; ASSOCIATION WEIGHT MATRIX; GENE; GENETIC ASSOCIATION; PHENOTYPE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84883142818     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-447-0_20     Document Type: Article

References (13)

1. Fortes MRS et al (2010) Association weight matrix for the genetic dissection of puberty in beef cattle. Proc Natl Acad Sci USA 107:13642-13647
2. Fortes MRS et al (2010) A new method for exploring genome-wide associations applied to cattle puberty. 9th World Congress on genetics applied to livestock production. German Society for Animal Science, Leipzig, Germany, pp 4-166. ISBN 978-3-00-031608-1.
3. Fortes MRS et al (2011) A single nucleotide polymorphism-derived regulatory gene network underlying puberty in 2 tropical breeds of beef cattle. J Anim Sci 89:1669-1683
4. Hudson NJ, Reverter A, Dalrymple BP (2009) A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Comput Biol 5: E1000382
5. Reverter A et al (2010) Regulatory impact factors: Unraveling the transcriptional regulation of complex traits from expression data. Bioinformatics 26:896-904
6. Reverter A, Chan EKF (2008) Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks. Bioinformatics 24:2491-2497
7. Cookson W et al (2009) Mapping complex disease traits with global gene expression. Nat Rev Genet 10:184-194
8. Caraux G, Pinloche S (2005) Permutmatrix: A graphical environment to arrange gene expression profiles in optimal linear order. Bioinformatics 21:1280-1281
9. Watson-Haigh NS, Kadarmideen HN, Reverter A (2010) PCIT: An R package for weighted gene co-expression networks based on partial correlation and information theory approaches. Bioinformatics 26:411-413
10. Shannon P et al (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-2504
11. Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:2
12. Snelling WM et al (2012) How SNP chips will advance our knowledge of factors controlling puberty and aid in selecting replacement beef females. J Anim Sci 90(4):1152-1165. doi:10.2527/jas.2011-4581
13. Weller JI, RonM(2011) Invited review: Quantitative trait nucleotide determination in the era of genomic selection. J Dairy Sci 94:1082-1090