View Full Document

6 views

Unformatted text preview:

Eigengene Network Analysis Four Tissues Of Female Mice R Tutorial Peter Langfelder and Steve Horvath Correspondence shorvath mednet ucla edu Peter Langfelder gmail com This is a self contained R software tutorial that illustrates how to carry out an eigengene network analysis across four corresponding to gene expression measurements in the brain muscle liver and adipose tissues of female mice of an F2 mouse cross The R code shows how to perform the analysis reported in Langelder and Horvath 2007 Some familiarity with the R software is desirable but the document is fairly self contained The methods and biological implications are described in the following refence Langfelder P Horvath S 2007 Eigengene networks for studying the relationships between co expression modules BMC Systems Biology This tutorial and the data files can be found at http www genetics ucla edu labs horvath CoexpressionNetwork EigengeneNetwork More material on weighted network analysis can be found at http www genetics ucla edu labs horvath CoexpressionNetwork For a detailed description of the mouse intercross see Wang et al 2006 A description of the microarray data can be found in Ghazalpour et al 2006 To facilitate comparison with the original analysis of Ghazalpour et al 2006 we used the same gene selection in our analysis Microarray Data The Agilent microarrays measured gene expression profiles in female mice of an F2 mouse intercross described in Ghazalpour et al 2006 The F2 mouse intercross data set referred to as B H cross involved 135 female mice derived from the F2 intercross between inbred strains C3H HeJ and C57BL 6J Ghazalpour et al 2006 Wang et al 2006 B H mice are ApoE null ApoE and thus hyperlipidemic and were fed a high fat diet The B H mice were sacrificed at 24 weeks Microarray analysis RNA preparation and array hybridizations were performed at Rosetta Inpharmatics Seattle Washington United States The custom ink jet microarrays used in this study Agilent Technologies Palo Alto



Access the best Study Guides, Lecture Notes and Practice Exams

Loading Unlocking...
Login

Join to view Eigengene Network Analysis and access 3M+ class-specific study document.

or
We will never post anything without your permission.
Don't have an account?
Sign Up

Join to view Eigengene Network Analysis and access 3M+ class-specific study document.

or

By creating an account you agree to our Privacy Policy and Terms Of Use

Already a member?