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

Reverter, Antonio and Fortes, Marina R. S. (2013). Association weight matrix: a network-based approach towards functional genome-wide association studies. In Genome-wide association studies and genomic prediction (pp. 437-447) New York, NY, United States: Humana Press. doi:10.1007/978-1-62703-447-0_20


Author Reverter, Antonio
Fortes, Marina R. S.
Title of chapter Association weight matrix: a network-based approach towards functional genome-wide association studies
Title of book Genome-wide association studies and genomic prediction
Place of Publication New York, NY, United States
Publisher Humana Press
Publication Year 2013
Sub-type Research book chapter (original research)
DOI 10.1007/978-1-62703-447-0_20
Series Methods in Molecular Biology
ISBN 9781627034463
ISSN 1064-3745
Volume number 1019
Chapter number 20
Start page 437
End page 447
Total pages 11
Total chapters 26
Collection year 2014
Subjects 1312 Molecular Biology
1311 Genetics
Abstract/Summary In this chapter we describe the Association Weight Matrix (AWM), a novel procedure to exploit the results from genome-wide association studies (GWAS) and, in combination with network inference algorithms, generate gene networks with regulatory and functional significance. In simple terms, the AWM is a matrix with rows represented by genes and columns represented by phenotypes. Individual {i, j}th elements in the AWM correspond to the association of the SNP in the ith gene to the jth phenotype. While our main objective is to provide a recipe-like tutorial on how to build and use AWM, we also take the opportunity to briefly reason the logic behind each step in the process. To conclude, we discuss the impact on AWM of issues like the number of phenotypes under scrutiny, the density of the SNP chip and the choice of contrast upon which to infer the cause-effect regulatory interactions.
Keyword Complex multivariate phenotypes
Gene network
Genome-wide association studies
Pathway analysis
Systems biology
Transcription factor analysis
Q-Index Code BX
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Book Chapter
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