Content of tutorial I
A. Gene Co-expression Network Construction
B. Module Definition Based on Average Linkage hierarchical clustering with the
dynamic tree cut algorithm
C. Relating Modules To Physiological Traits (module significance analysis)
D. Comparing Weighted Network Results to Unweighted Network Results
E. Studying the Clustering Coefficicient
First Tutorial Word Document
Microsoft word version
PDF version
Relevant Data (Zipped Tutorial1)
Content of tutorial II
A. Robustness of network modules and connectivity with respect to removing
microrray samples
B. Preservation of module and connectivity across multiple gender tissue
combinations
Second Tutorial Word Document
Microsoft word version
Relevant Data (Zipped Tutorial2)
Content of tutorial III
A. Relating the 22 clinical traits and the expression profiles to genetic SNP
markers Quantitative trait locus, LODscore, QTL, linkage analysis, allelic
association analysis, mQTL
B. LOD score curve and mQTL graph (Figure 3)
C. Regress a phenotype on multiple markers with the fitqtl package
Third
Tutorial Word Document
Microsoft word version
Relevant Data (Zipped Tutorial3)
Content of tutorial IV
A. Network properties are integrated with genetic information to characterize
weight related genes of the blue module
B. Multivariable regression models that regress the body weight based gene
significance (GSweight) on SNP significance measures (GSmQTL) and intramodular
connectivity (k)
Fourth Tutorial Word Document
Microsoft word version
Relevant Data (Zipped Tutorial4)
Content of tutorial V
A. A simulated gene co-expression network to illustrate the use of the
topological overlap matrix for module detection
Fourth
Tutorial Word Document
Microsoft word version (recommended)
PDF version
Talk on this application
PowerPoint version
PDF version
Download the following R function file, which contains several R functions
needed for Weighted Gene Co-Expression Network Analysis.
Network
R functions
Weighted Gene Co-Expression Network Page
The weighted gene co-expression network analysis method is described in Theory Paper 1: Zhang and Horvath (2005)
For a more mathematical description of weighted gene co-expression networks consider Theory Papers: Dong and Horvath (2007, 2008)
2008-11-12
Please send your suggestions and
comments to: shorvath@mednet.ucla.edu