scholarly journals Regulatory Network Identification by Genetical Genomics: Signaling Downstream of the Arabidopsis Receptor-Like Kinase ERECTA

2010 ◽  
Vol 154 (3) ◽  
pp. 1067-1078 ◽  
Author(s):  
Inez R. Terpstra ◽  
L. Basten Snoek ◽  
Joost J.B. Keurentjes ◽  
Anton J.M. Peeters ◽  
Guido Van den Ackerveken
Keyword(s):  
Regulatory Network ◽  
Genetical Genomics ◽  
Receptor Like Kinase ◽  
Network Identification

scholarly journals The GAGA factor regulatory network: Identification of GAGA factor associated proteins

PLoS ONE ◽  
2017 ◽  
Vol 12 (3) ◽  
pp. e0173602 ◽  
Author(s):  
Dmitry Lomaev ◽  
Anna Mikhailova ◽  
Maksim Erokhin ◽  
Alexander V. Shaposhnikov ◽  
James J. Moresco ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Gaga Factor ◽  
Associated Proteins ◽  
Network Identification

Inferring Gene Regulatory Networks from Genetical Genomics Data

2010 ◽  
pp. 79-107 ◽  
Author(s):  
Bing Liu ◽  
Ina Hoeschele ◽  
Alberto de la Fuente
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Network Inference ◽  
Dna Marker ◽  
Search Space ◽  
Genetical Genomics ◽  
Gene Regulatory Network Inference ◽  
Gene Regulatory

In this chapter, we review the current state of Gene Regulatory Network inference based on ‘Genetical Genomics’ experiments (Brem & Kruglyak, 2005; Brem, Yvert, Clinton & Kruglyak, 2002; Jansen, 2003; Jansen & Nap, 2001; Schadt et al., 2003) as a special case of causal network inference in ‘Systems Genetics’ (Threadgill, 2006). In a Genetical Genomics experiment, a segregating or genetically randomized population is DNA marker genotyped and gene-expression profiled on a genomewide scale. The genotypes are regarded as natural, multifactorial perturbations resulting in different gene-expression ‘phenotypes’, and causal relationships can therefore be established between the measured genotypes and the gene-expression phenotypes. In this chapter, we review different computational approaches to Gene Regulatory Network inference based on the joint analysis of DNA marker and expression data and additionally of DNA sequence information if available. This includes different methods for expression QTL mapping, selection of regulator-target pairs, construction of an encompassing network, which strongly constrains the network search space, and pairwise and multivariate methods for Gene Regulatory Network inference, such as Bayesian Networks and Structural Equation Modeling.

Sign in / Sign up

Export Citation Format

Share Document