lncBodyMap   >>  


 

Stomach: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Stomach 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

 

 

Notable Pathways:

To facilitate network analysis of the Stomach 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
 M8  GO ORGANELLE FISSION   83/289   2.43E-56  83  366  27  cyjs file 
 M8  GO CELL DIVISION   77/289   2.78E-52  77  366  27  cyjs file 
 M8  GO CHROMOSOME SEGREGATION   55/289   6.82E-41  55  366  27  cyjs file 
 M8  GO NUCLEAR CHROMOSOME SEGREGATION   50/289   7.48E-39  50  366  27  cyjs file 
 M8  GO CHROMOSOMAL REGION   57/289   1.19E-38  57  366  27  cyjs file 
 M8  GO SISTER CHROMATID SEGREGATION   45/289   4.36E-38  45  366  27  cyjs file 
 M8  GO CONDENSED CHROMOSOME   43/289   2.26E-33  43  366  27  cyjs file 
 M8  GO CELL CYCLE PHASE TRANSITION   46/289   1.00E-31  46  366  27  cyjs file 
 M8  GO CHROMOSOME CENTROMERIC REGION   39/289   1.78E-30  39  366  27  cyjs file 
 M8  GO DNA REPLICATION   41/289   9.07E-30  41  366  27  cyjs file 
 M21  GO LYMPHOCYTE ACTIVATION   34/113   7.00E-28  34  158  26  cyjs file 
 M21  GO LEUKOCYTE ACTIVATION   36/113   7.00E-28  36  158  26  cyjs file 
 M8  GO CELL CYCLE CHECKPOINT   35/289   6.35E-24  35  366  27  cyjs file 
 M8  GO DNA CONFORMATION CHANGE   37/289   6.46E-21  37  366  27  cyjs file 
 M8  GO DNA REPAIR   47/289   8.72E-21  47  366  27  cyjs file 
 M8  GO SPINDLE   37/289   4.21E-20  37  366  27  cyjs file 
 M8  GO REGULATION OF CELL DIVISION   36/289   4.83E-20  36  366  27  cyjs file 
 M21  GO REGULATION OF CELL ACTIVATION   31/113   8.31E-20  31  158  26  cyjs file 
 M8  GO REGULATION OF MICROTUBULE BASED PROCESS   34/289   1.12E-19  34  366  27  cyjs file 
 M8  GO MICROTUBULE CYTOSKELETON ORGANIZATION   37/289   2.13E-17  37  366  27  cyjs file 
 M8  GO REGULATION OF CELL CYCLE PHASE TRANSITION   34/289   5.98E-16  34  366  27  cyjs file 
 M8  GO NEGATIVE REGULATION OF ORGANELLE ORGANIZATION   37/289   5.98E-16  37  366  27  cyjs file 
 M8  GO NEGATIVE REGULATION OF CELL CYCLE   38/289   3.26E-15  38  366  27  cyjs file 
 M8  GO POSITIVE REGULATION OF CELL CYCLE   32/289   7.18E-14  32  366  27  cyjs file 
 M8  GO CENTROSOME   37/289   7.25E-13  37  366  27  cyjs file