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Lung: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Lung 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
    M34 module
    M35 module
    M36 module
    M37 module
    M38 module
    M39 module
    M40 module
    M41 module
    M42 module
    M43 module
    M44 module
    M45 module
    M46 module
    M47 module
    M48 module
    M49 module

 

 

Notable Pathways:

To facilitate network analysis of the Lung 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 ANTIGEN PROCESSING AND PRESENTATION   33/1040   0.000145179  33  1584  266  cyjs file 
 M1  GO REGULATION OF CELLULAR PROTEIN CATABOLIC PROCESS   32/1040   0.013471981  32  1584  266  cyjs file 
 M1  GO ER TO GOLGI VESICLE MEDIATED TRANSPORT   28/1040   0.000167168  28  1584  266  cyjs file 
 M1  GO POSITIVE REGULATION OF WNT SIGNALING PATHWAY   25/1040   0.000560904  25  1584  266  cyjs file 
 M17  GO CELL SUBSTRATE JUNCTION   44/251   3.29E-24  44  330  39  cyjs file 
 M17  GO ANCHORING JUNCTION   44/251   1.40E-20  44  330  39  cyjs file 
 M21  GO REGULATION OF MICROTUBULE BASED PROCESS   30/227   9.76E-19  30  286  28  cyjs file 
 M21  GO REGULATION OF CELL DIVISION   29/227   2.24E-16  29  286  28  cyjs file 
 M25  GO LYMPHOCYTE ACTIVATION   32/141   3.13E-22  32  204  35  cyjs file 
 M36  GO EXTRACELLULAR MATRIX   31/71   3.24E-28  31  103  15  cyjs file 
 M4  GO CELL PROJECTION ASSEMBLY   72/575   1.28E-42  72  1064  208  cyjs file 
 M4  GO MICROTUBULE CYTOSKELETON ORGANIZATION   44/575   4.07E-12  44  1064  208  cyjs file 
 M4  GO MOTILE CILIUM   30/575   2.70E-17  30  1064  208  cyjs file 
 M6  GO ANCHORING JUNCTION   36/629   0.012488934  36  983  196  cyjs file 
 M6  GO ENDOTHELIAL CELL DEVELOPMENT   10/629   0.003928291  10  983  196  cyjs file 
 M6  GO VASCULATURE DEVELOPMENT   44/629   4.70E-05  44  983  196  cyjs file 
 M6  GO EPITHELIAL CELL DIFFERENTIATION   35/629   0.022586014  35  983  196  cyjs file 
 M6  GO REGULATION OF RESPONSE TO WOUNDING   34/629   0.005747472  34  983  196  cyjs file 
 M6  GO REGULATION OF CELL ACTIVATION   34/629   0.027714217  34  983  196  cyjs file 
 M6  GO MORPHOGENESIS OF AN EPITHELIUM   29/629   0.034259292  29  983  196  cyjs file 
 M7  GO CELL CELL JUNCTION   35/552   0.000116548  35  908  196  cyjs file 
 M7  GO MORPHOGENESIS OF AN EPITHELIUM   33/552   0.000610523  33  908  196  cyjs file 
 M7  GO GLYCEROLIPID METABOLIC PROCESS   30/552   0.000893484  30  908  196  cyjs file 
 M7  GO PHOSPHOLIPID METABOLIC PROCESS   30/552   0.001094275  30  908  196  cyjs file