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Pancreas: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Pancreas 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

 

 

Notable Pathways:

To facilitate network analysis of the Pancreas 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
 M11  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO MEMBRANE   85/314   8.49E-82  85  426  55  cyjs file 
 M11  GO PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   81/314   1.40E-110  81  426  55  cyjs file 
 M5  GO CELL SUBSTRATE JUNCTION   54/792   6.43E-10  54  1030  89  cyjs file 
 M5  GO BLOOD VESSEL MORPHOGENESIS   53/792   9.05E-11  53  1030  89  cyjs file 
 M5  GO EPITHELIAL CELL DIFFERENTIATION   50/792   2.06E-05  50  1030  89  cyjs file 
 M5  GO RESPONSE TO GROWTH FACTOR   48/792   3.03E-05  48  1030  89  cyjs file 
 M6  GO REGULATION OF HORMONE LEVELS   48/561   8.75E-09  48  876  127  cyjs file 
 M6  GO SECRETION BY CELL   47/561   3.66E-08  47  876  127  cyjs file 
 M5  GO REGULATION OF CYTOPLASMIC TRANSPORT   45/792   0.000310579  45  1030  89  cyjs file 
 M5  GO ENZYME ACTIVATOR ACTIVITY   42/792   0.001277054  42  1030  89  cyjs file 
 M5  GO SECRETION BY CELL   42/792   0.002143871  42  1030  89  cyjs file 
 M5  GO SMALL GTPASE MEDIATED SIGNAL TRANSDUCTION   37/792   0.000173214  37  1030  89  cyjs file 
 M5  GO ENZYME INHIBITOR ACTIVITY   37/792   0.000638397  37  1030  89  cyjs file 
 M5  GO SIDE OF MEMBRANE   37/792   0.004148003  37  1030  89  cyjs file 
 M6  GO REGULATION OF VESICLE MEDIATED TRANSPORT   33/561   0.00164863  33  876  127  cyjs file 
 M6  GO SIGNAL RELEASE   31/561   3.18E-11  31  876  127  cyjs file 
 M6  GO TRANSPORT VESICLE   31/561   6.20E-05  31  876  127  cyjs file 
 M6  GO ORGANELLE LOCALIZATION   31/561   0.001358029  31  876  127  cyjs file 
 M5  GO EXTRACELLULAR STRUCTURE ORGANIZATION   52/792   7.19E-13  52  1030  89  cyjs file 
 M1  GO POSITIVE REGULATION OF CATABOLIC PROCESS   60/1735   0.037478825  60  2694  431  cyjs file 
 M1  GO ATPASE ACTIVITY COUPLED   59/1735   0.000370039  59  2694  431  cyjs file 
 M1  GO NEGATIVE REGULATION OF ORGANELLE ORGANIZATION   59/1735   0.037478825  59  2694  431  cyjs file 
 M1  GO MITOTIC NUCLEAR DIVISION   58/1735   0.016490908  58  2694  431  cyjs file 
 M5  GO ACTIN CYTOSKELETON   45/792   5.64E-05  45  1030  89  cyjs file