Supplementary Material for

Mason MJ, Fan G, Plath K, Zhou Q, Horvath S (2009)

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells

BMC Genomics 2009, 10:327.

Link To Paper: http://www.biomedcentral.com/1471-2164/10/327/

Contents

R code and data for generating Figures and Tables with the Ivanova Data Set.

R Code

• signedWGCNAivanova.R

• NetworkFunctions.txt

• CustomFunctions.txt

Ivanova et al (2006) Gene Expression and Significance Data

• dataIdsNsignifsIvanova.txt

• IvanovaData.txt

Affymetrix Micro-array and Mm8 Annotations

• Mouse430_2simpleAnnotWid.txt

• refFlat.txt

ChIP-Seq, ChIP-Chip, and ChIP-PET TF Binding Data

• ngSuppBinding.txt

• BoyerBoundData.txt

• Oct4_ChIPPED_Assorefseqinfo.txt

• Nanog_ChIPPED_Assorefseqinfo_delN.txt

Zhou et al (2007) Gene Classification Data

• zhouOct4RiMinus.txt

• zhouOct4RiPlus.txt

• zhouRAminus.txt

• zhouRAplus.txt

Compressed Output Folder Containing Files that Should be Generated by Code

• output.zip