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Thyroid: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Thyroid 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
    M14 module
    M15 module
    M16 module
    M17 module
    M18 module
    M19 module
    M20 module
    M21 module
    M22 module
    M23 module
    M24 module
    M25 module
    M26 module
    M27 module
    M28 module
    M29 module
    M30 module
    M31 module
    M32 module
    M33 module



Notable Pathways:

To facilitate network analysis of the Thyroid 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
 M1  GO LYMPHOCYTE ACTIVATION   105/1243   2.44e-35  105  1990  408  cyjs file 
 M1  GO LEUKOCYTE ACTIVATION   113/1243   3.72e-33  113  1990  408  cyjs file 
 M1  GO REGULATION OF CELL ACTIVATION   116/1243   1.64e-28  116  1990  408  cyjs file 
 M1  GO LEUKOCYTE CELL CELL ADHESION   77/1243   3.16e-25  77  1990  408  cyjs file 
 M1  GO SIDE OF MEMBRANE   101/1243   3.87e-24  101  1990  408  cyjs file 
 M1  GO REGULATION OF HOMOTYPIC CELL CELL ADHESION   80/1243   9.37e-22  80  1990  408  cyjs file 
 M1  GO SINGLE ORGANISM CELL ADHESION   101/1243   9.46e-22  101  1990  408  cyjs file 
 M1  GO POSITIVE REGULATION OF CELL ACTIVATION   79/1243   8.15e-21  79  1990  408  cyjs file 
 M1  GO REGULATION OF CELL CELL ADHESION   88/1243   2.03e-20  88  1990  408  cyjs file 
 M1  GO REGULATION OF LEUKOCYTE PROLIFERATION   62/1243   2.94e-20  62  1990  408  cyjs file 
 M1  GO LEUKOCYTE DIFFERENTIATION   74/1243   1.82e-19  74  1990  408  cyjs file 
 M4  GO MRNA PROCESSING   69/707   6.00e-19  69  1183  227  cyjs file 
 M1  GO LYMPHOCYTE DIFFERENTIATION   60/1243   1.75e-18  60  1990  408  cyjs file 
 M1  GO POSITIVE REGULATION OF CELL CELL ADHESION   64/1243   1.16e-17  64  1990  408  cyjs file 
 M4  GO RNA SPLICING   61/707   1.22e-17  61  1183  227  cyjs file 
 M1  GO POSITIVE REGULATION OF CELL ADHESION   80/1243   3.00e-16  80  1990  408  cyjs file 
 M1  GO NEGATIVE REGULATION OF IMMUNE SYSTEM PROCESS   77/1243   6.73e-15  77  1990  408  cyjs file 
 M2  GO OXIDATIVE PHOSPHORYLATION   33/1138   2.07e-14  33  1898  382  cyjs file 
 M1  GO REGULATION OF LEUKOCYTE MEDIATED IMMUNITY   45/1243   8.57e-14  45  1990  408  cyjs file 
 M1  GO REGULATION OF T CELL PROLIFERATION   43/1243   2.11e-13  43  1990  408  cyjs file 
 M1  GO T CELL DIFFERENTIATION   39/1243   2.18e-13  39  1990  408  cyjs file 
 M1  GO ADAPTIVE IMMUNE RESPONSE   62/1243   1.03e-12  62  1990  408  cyjs file 
 M2  GO ELECTRON TRANSPORT CHAIN   32/1138   2.41e-12  32  1898  382  cyjs file 
 M1  GO NEGATIVE REGULATION OF CELL ACTIVATION   43/1243   2.97e-12  43  1990  408  cyjs file 
 M1  GO POSITIVE REGULATION OF LEUKOCYTE PROLIFERATION   39/1243   7.39e-12  39  1990  408  cyjs file