lncBodyMap   >>  


 

Esophagus: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Esophagus 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

 

 

Notable Pathways:

To facilitate network analysis of the Esophagus 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 GOLGI VESICLE TRANSPORT   77/2522   0.00694033  77  3814  567  cyjs file 
 M7  GO ORGANELLE FISSION   75/268   1.10E-49  75  342  25  cyjs file 
 M1  GO TUBE MORPHOGENESIS   72/2522   0.042522044  72  3814  567  cyjs file 
 M2  GO ACTIN FILAMENT BASED PROCESS   64/1129   1.79E-06  64  1764  320  cyjs file 
 M2  GO ACTIN CYTOSKELETON   61/1129   9.77E-06  61  1764  320  cyjs file 
 M2  GO MUSCLE STRUCTURE DEVELOPMENT   58/1129   3.97E-05  58  1764  320  cyjs file 
 M4  GO ANCHORING JUNCTION   55/674   3.73E-09  55  917  95  cyjs file 
 M2  GO MUSCLE SYSTEM PROCESS   54/1129   1.96E-09  54  1764  320  cyjs file 
 M2  GO ACTIN BINDING   54/1129   4.72E-05  54  1764  320  cyjs file 
 M2  GO CONTRACTILE FIBER   50/1129   4.44E-12  50  1764  320  cyjs file 
 M2  GO MUSCLE CONTRACTION   47/1129   4.37E-09  47  1764  320  cyjs file 
 M7  GO CELL CYCLE PHASE TRANSITION   47/268   2.12E-34  47  342  25  cyjs file 
 M3  GO REGULATION OF MITOTIC CELL CYCLE   42/869   0.030068597  42  1274  192  cyjs file 
 M3  GO ANCHORING JUNCTION   42/869   0.043009524  42  1274  192  cyjs file 
 M4  GO GOLGI VESICLE TRANSPORT   42/674   7.21E-09  42  917  95  cyjs file 
 M4  GO CELL CELL JUNCTION   39/674   1.58E-05  39  917  95  cyjs file 
 M4  GO EPITHELIAL CELL DIFFERENTIATION   39/674   0.002114324  39  917  95  cyjs file 
 M4  GO ACTIN FILAMENT BASED PROCESS   38/674   0.000970561  38  917  95  cyjs file 
 M2  GO REGULATION OF MUSCLE SYSTEM PROCESS   37/1129   1.79E-06  37  1764  320  cyjs file 
 M2  GO EXTRACELLULAR STRUCTURE ORGANIZATION   36/1129   0.020039509  36  1764  320  cyjs file 
 M3  GO CELL SUBSTRATE JUNCTION   36/869   0.042941045  36  1274  192  cyjs file 
 M7  GO MICROTUBULE CYTOSKELETON ORGANIZATION   32/268   3.32E-14  32  342  25  cyjs file 
 M2  GO REGULATION OF MUSCLE CONTRACTION   30/1129   7.15E-06  30  1764  320  cyjs file 
 M2  GO CELL JUNCTION ORGANIZATION   30/1129   0.000600635  30  1764  320  cyjs file