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Skin: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Skin RNA-seq resulted in identification of modules comprising of protein coding genes and lncRNAs with correlated expression patterns. The genes in the coexpression modules were subjected to pathway enrichment to identify pathways in which the genes in the modules significantly enrich. Shown below is a graphical summary comprising of the modules and the pathways terms to which the genes in the respective module associate with. Viewers can shortlist the modules of interest based on the biological process of interest.

 

Graphical Summary of WGCNA modules

 

Significant Modules/Pathways

Genes in the coexpression modules identified by WGCNA analysis were further analyzed for pathway enrichment. All the pathways in which the genes from the coexpression modules significantly (q value < 0.05) enrich for are presented below. Viewers can browse the table or search for key pathway terms in the "search" window.
Full pathway enrichment results and the adjacency matrix of the modules of interest can be downloaded below:
Download: [ Modules Full list (CSV), Adjacency Matrices (tar.gz) ] or 
Adjacency Matrix per Module:
    M1 module
    M2 module
    M3 module
    M4 module
    M5 module
    M6 module
    M7 module
    M8 module
    M9 module
    M10 module
    M11 module
    M12 module
    M13 module

 

 

Notable Pathways:

To facilitate network analysis of the Skin RNA seq data, 25 notable pathways from the pathway enrichment data was selected. For each pathway, network image and json file was generated that comprises of the gene (in the indicated pathway) along with correlated lncRNAs. Viewers can look at the PNG file to view the network of download and open the cyjs file in Cytoscape for further exploration. (Green circular nodes: protein-coding genes, Orange triangle: lncRNAs)
 Module   ID  Gene Ratio  qvalue  Gene Count  Total Genes in module   lncrnas in module   Plot  Cytoscape JSON file
 M12  GO ANCHORING JUNCTION   289/6551   1.41E-17  289  7974  4403  cyjs file 
 M12  GO VASCULATURE DEVELOPMENT   276/6551   8.74E-17  276  7974  4403  cyjs file 
 M12  GO CELL SUBSTRATE JUNCTION   232/6551   2.37E-13  232  7974  4403  cyjs file 
 M12  GO ACTIN FILAMENT BASED PROCESS   232/6551   1.13E-06  232  7974  4403  cyjs file 
 M12  GO SKELETAL SYSTEM DEVELOPMENT   230/6551   7.01E-06  230  7974  4403  cyjs file 
 M12  GO ENDOMEMBRANE SYSTEM ORGANIZATION   230/6551   4.49E-05  230  7974  4403  cyjs file 
 M12  GO EPITHELIAL CELL DIFFERENTIATION   221/6551   0.022021549  221  7974  4403  cyjs file 
 M12  GO REGULATION OF VESICLE MEDIATED TRANSPORT   218/6551   0.001690139  218  7974  4403  cyjs file 
 M12  GO REGULATION OF PROTEIN SERINE THREONINE KINASE ACTIVITY   218/6551   0.004116847  218  7974  4403  cyjs file 
 M12  GO SINGLE ORGANISM CELL ADHESION   217/6551   0.001562985  217  7974  4403  cyjs file 
 M12  GO REGULATION OF RESPONSE TO WOUNDING   186/6551   0.026933782  186  7974  4403  cyjs file 
 M12  GO REGULATION OF PROTEIN CATABOLIC PROCESS   185/6551   0.004614238  185  7974  4403  cyjs file 
 M12  GO REGULATION OF CELL GROWTH   184/6551   0.004774655  184  7974  4403  cyjs file 
 M12  GO WNT SIGNALING PATHWAY   163/6551   0.013981189  163  7974  4403  cyjs file 
 M12  GO MEMBRANE MICRODOMAIN   137/6551   0.011358949  137  7974  4403  cyjs file 
 M12  GO CELL PROJECTION MEMBRANE   137/6551   0.033944996  137  7974  4403  cyjs file 
 M12  GO CELLULAR RESPONSE TO EXTERNAL STIMULUS   136/6551   0.000439889  136  7974  4403  cyjs file 
 M12  GO ADHERENS JUNCTION ORGANIZATION   42/6551   0.005754623  42  7974  4403  cyjs file 
 M12  GO ER TO GOLGI TRANSPORT VESICLE   42/6551   0.005754623  42  7974  4403  cyjs file 
 M12  GO REGULATION OF EPITHELIAL TO MESENCHYMAL TRANSITION   37/6551   0.0326053  37  7974  4403  cyjs file 
 M12  GO POSITIVE REGULATION OF ENDOTHELIAL CELL PROLIFERATION   37/6551   0.039351278  37  7974  4403  cyjs file 
 M12  GO NEGATIVE REGULATION OF CELL SUBSTRATE ADHESION   31/6551   0.023951162  31  7974  4403  cyjs file 
 M12  GO NEGATIVE REGULATION OF EPITHELIAL CELL MIGRATION   31/6551   0.023951162  31  7974  4403  cyjs file 
 M13  GO REGULATION OF CELL CYCLE PHASE TRANSITION   47/553   3.72E-16  47  644  181  cyjs file