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Colon: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Colon 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

 

 

Notable Pathways:

To facilitate network analysis of the Colon 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 APOPTOTIC SIGNALING PATHWAY   172/8246   0.003053772  172  12733  2138  cyjs file 
 M1  GO FATTY ACID METABOLIC PROCESS   170/8246   0.017083098  170  12733  2138  cyjs file 
 M1  GO REGULATION OF EPITHELIAL CELL PROLIFERATION   162/8246   0.030607122  162  12733  2138  cyjs file 
 M1  GO REGULATION OF MICROTUBULE BASED PROCESS   143/8246   0.012914944  143  12733  2138  cyjs file 
 M1  GO NEGATIVE REGULATION OF CYTOSKELETON ORGANIZATION   132/8246   0.010246569  132  12733  2138  cyjs file 
 M1  GO MICROTUBULE BINDING   130/8246   0.000229189  130  12733  2138  cyjs file 
 M1  GO CONTRACTILE FIBER   130/8246   0.002843589  130  12733  2138  cyjs file 
 M1  GO MICROTUBULE BASED MOVEMENT   125/8246   0.00534397  125  12733  2138  cyjs file 
 M1  GO NEGATIVE REGULATION OF MITOTIC CELL CYCLE   119/8246   0.01450105  119  12733  2138  cyjs file 
 M1  GO CELL JUNCTION ORGANIZATION   114/8246   0.005551813  114  12733  2138  cyjs file 
 M1  GO ESTABLISHMENT OR MAINTENANCE OF CELL POLARITY   95/8246   0.000386105  95  12733  2138  cyjs file 
 M1  GO CELL CYCLE ARREST   95/8246   0.012633907  95  12733  2138  cyjs file 
 M1  GO CELL CYCLE G2 M PHASE TRANSITION   93/8246   0.000425473  93  12733  2138  cyjs file 
 M1  GO CELL JUNCTION ASSEMBLY   88/8246   0.000391835  88  12733  2138  cyjs file 
 M1  GO LIPOSACCHARIDE METABOLIC PROCESS   80/8246   0.000229189  80  12733  2138  cyjs file 
 M1  GO FILOPODIUM   59/8246   0.041517963  59  12733  2138  cyjs file 
 M1  GO FATTY ACID CATABOLIC PROCESS   52/8246   0.002760985  52  12733  2138  cyjs file 
 M1  GO REGULATION OF SODIUM ION TRANSPORT   50/8246   0.033563901  50  12733  2138  cyjs file 
 M1  GO POSITIVE REGULATION OF CELL CYCLE PHASE TRANSITION   47/8246   0.01063945  47  12733  2138  cyjs file 
 M1  GO REGULATION OF CELL JUNCTION ASSEMBLY   47/8246   0.01063945  47  12733  2138  cyjs file 
 M2  GO REGULATION OF CYTOPLASMIC TRANSPORT   46/1006   0.031614637  46  1599  297  cyjs file 
 M3  GO IMMUNE EFFECTOR PROCESS   45/603   4.94E-07  45  847  125  cyjs file 
 M2  GO AUTOPHAGY   44/1006   0.003221256  44  1599  297  cyjs file 
 M3  GO SECRETION BY CELL   41/603   1.42E-05  41  847  125  cyjs file