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Adipose_Tissue: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Adipose_Tissue 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

 

 

Notable Pathways:

To facilitate network analysis of the Adipose_Tissue 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
 M15  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE   84/244   3.90E-78  84  338  40  cyjs file 
 M15  GO RIBOSOME   82/244   5.18E-94  82  338  40  cyjs file 
 M15  GO MULTI ORGANISM METABOLIC PROCESS   81/244   5.60E-115  81  338  40  cyjs file 
 M15  GO NUCLEAR TRANSCRIBED MRNA CATABOLIC PROCESS NONSENSE MEDIATED DECAY   78/244   1.49E-116  78  338  40  cyjs file 
 M4  GO MITOCHONDRIAL MATRIX   73/938   1.12E-15  73  1432  221  cyjs file 
 M3  GO VASCULATURE DEVELOPMENT   51/944   0.000309486  51  1490  282  cyjs file 
 M6  GO GENERATION OF PRECURSOR METABOLITES AND ENERGY   51/590   1.12E-19  51  959  166  cyjs file 
 M4  GO GLYCOSYL COMPOUND METABOLIC PROCESS   47/938   1.82E-05  47  1432  221  cyjs file 
 M3  GO GLYCEROLIPID METABOLIC PROCESS   46/944   1.82E-05  46  1490  282  cyjs file 
 M3  GO RESPONSE TO EXTRACELLULAR STIMULUS   44/944   0.005203356  44  1490  282  cyjs file 
 M3  GO BLOOD VESSEL MORPHOGENESIS   43/944   0.000249431  43  1490  282  cyjs file 
 M4  GO COFACTOR METABOLIC PROCESS   43/938   4.62E-05  43  1432  221  cyjs file 
 M3  GO REGULATION OF HORMONE LEVELS   42/944   0.044222027  42  1490  282  cyjs file 
 M3  GO ALCOHOL METABOLIC PROCESS   41/944   0.000363035  41  1490  282  cyjs file 
 M3  GO PHOSPHOLIPID METABOLIC PROCESS   41/944   0.000924048  41  1490  282  cyjs file 
 M3  GO REGULATION OF LIPID METABOLIC PROCESS   39/944   2.69E-05  39  1490  282  cyjs file 
 M3  GO GLYCEROPHOSPHOLIPID METABOLIC PROCESS   35/944   0.001449879  35  1490  282  cyjs file 
 M3  GO LIPID LOCALIZATION   31/944   0.003447341  31  1490  282  cyjs file 
 M3  GO GLYCEROLIPID BIOSYNTHETIC PROCESS   30/944   0.000237295  30  1490  282  cyjs file 
 M3  GO LIPID CATABOLIC PROCESS   30/944   0.002703041  30  1490  282  cyjs file 
 M3  GO CELLULAR LIPID CATABOLIC PROCESS   25/944   0.000116761  25  1490  282  cyjs file 
 M3  GO LIPID MODIFICATION   25/944   0.009414201  25  1490  282  cyjs file 
 M13  GO RESPONSE TO STEROID HORMONE   24/331   0.006999727  24  521  99  cyjs file 
 M24  GO LEUKOCYTE CELL CELL ADHESION   22/107   1.22E-16  22  178  37  cyjs file