how to create a gene co-expression network?

Question

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I have stagewise file of genes(early stage)-

genename|EntrezGene|Startposition|Endposition|RefAllele|TumorSeqAllele|TumorSeqAllele2|sample   
    ABAT      18         8873373     8873373         G        G             A         TCGA- 6961
    ABAT      18         8873373     8873373         G        G             A         TCGA- 6961
    ABCA1     19         107593339   107593339       G        G             A         TCGA-6433
    ABCA2     20         139910481   139910481       C        C             T         TCGA-6961

i have also file of expression data-

entrez_Id   TCGA-6433   TCGA-6961   TCGA-4075   TCGA-4076
    ABAT     1228         8086         2950      1613
    ABAT0    0            0            1         0
    ABCA1    1254         8115         5510      2015
    ABCA2    270          776          355       553

how to create a gene-coexpression network using r language? what should be the input file?

[hafiz.talhamalik]

try R package CoRegNet [1]https://bioconductor.org/packages/release/bioc/html/CoRegNet.html

Answer 1

[Prakash]

you need to have a gene expression matrix and you can create co-expression network using WGCNA. https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/