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Prostate: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Prostate 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
    M50 module
    M51 module
    M52 module
    M53 module
    M54 module

 

 

Notable Pathways:

To facilitate network analysis of the Prostate 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
 M22  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE   83/185   6.87E-89  83  275  51  cyjs file 
 M22  GO MULTI ORGANISM METABOLIC PROCESS   80/185   7.66E-125  80  275  51  cyjs file 
 M22  GO PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   79/185   1.99E-128  79  275  51  cyjs file 
 M22  GO PROTEIN TARGETING TO MEMBRANE   79/185   2.62E-116  79  275  51  cyjs file 
 M22  GO RIBOSOMAL SUBUNIT   79/185   1.29E-114  79  275  51  cyjs file 
 M22  GO CYTOSOLIC PART   79/185   4.80E-101  79  275  51  cyjs file 
 M3  GO CELL SUBSTRATE JUNCTION   57/929   3.45E-08  57  1525  312  cyjs file 
 M3  GO ACTIN CYTOSKELETON   57/929   1.01E-06  57  1525  312  cyjs file 
 M3  GO ACTIN FILAMENT BASED PROCESS   55/929   7.14E-06  55  1525  312  cyjs file 
 M10  GO CONTRACTILE FIBER   52/360   2.14E-37  52  514  76  cyjs file 
 M10  GO MUSCLE SYSTEM PROCESS   46/360   9.13E-25  46  514  76  cyjs file 
 M3  GO EXTRACELLULAR MATRIX   46/929   0.001733202  46  1525  312  cyjs file 
 M10  GO MUSCLE STRUCTURE DEVELOPMENT   45/360   1.60E-16  45  514  76  cyjs file 
 M10  GO MUSCLE CONTRACTION   43/360   4.21E-25  43  514  76  cyjs file 
 M10  GO ACTIN CYTOSKELETON   43/360   1.28E-14  43  514  76  cyjs file 
 M10  GO ACTIN FILAMENT BASED PROCESS   43/360   1.92E-14  43  514  76  cyjs file 
 M22  GO CELL SUBSTRATE JUNCTION   42/185   6.47E-28  42  275  51  cyjs file 
 M22  GO ANCHORING JUNCTION   42/185   2.55E-24  42  275  51  cyjs file 
 M2  GO RIBOSOME BIOGENESIS   36/812   0.000172072  36  1528  449  cyjs file 
 M2  GO REGULATION OF PROTEIN CATABOLIC PROCESS   36/812   0.009395925  36  1528  449  cyjs file 
 M3  GO MUSCLE CONTRACTION   35/929   1.73E-05  35  1525  312  cyjs file 
 M3  GO EXTRACELLULAR STRUCTURE ORGANIZATION   35/929   0.005313468  35  1525  312  cyjs file 
 M3  GO PROTEINACEOUS EXTRACELLULAR MATRIX   35/929   0.044848312  35  1525  312  cyjs file 
 M2  GO GLYCOSYL COMPOUND METABOLIC PROCESS   33/812   0.020814103  33  1528  449  cyjs file 
 M2  GO NEGATIVE REGULATION OF ORGANELLE ORGANIZATION   33/812   0.03706313  33  1528  449  cyjs file