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Breast: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Breast 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

 

 

Notable Pathways:

To facilitate network analysis of the Breast 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 FATTY ACID METABOLIC PROCESS   66/1459   1.34E-10  66  2092  298  cyjs file 
 M1  GO COFACTOR BINDING   65/1459   2.25E-12  65  2092  298  cyjs file 
 M1  GO ANCHORING JUNCTION   65/1459   0.006200954  65  2092  298  cyjs file 
 M1  GO VASCULATURE DEVELOPMENT   60/1459   0.018728003  60  2092  298  cyjs file 
 M1  GO GLYCEROLIPID METABOLIC PROCESS   59/1459   4.66E-05  59  2092  298  cyjs file 
 M1  GO RESPONSE TO EXTRACELLULAR STIMULUS   59/1459   0.009226387  59  2092  298  cyjs file 
 M1  GO REGULATION OF HORMONE LEVELS   59/1459   0.038731187  59  2092  298  cyjs file 
 M2  GO ANCHORING JUNCTION   59/935   1.16E-05  59  1609  338  cyjs file 
 M1  GO NEGATIVE REGULATION OF INTRACELLULAR SIGNAL TRANSDUCTION   58/1459   0.01115719  58  2092  298  cyjs file 
 M1  GO COENZYME METABOLIC PROCESS   57/1459   1.32E-08  57  2092  298  cyjs file 
 M1  GO REGULATION OF LIPID METABOLIC PROCESS   56/1459   3.23E-07  56  2092  298  cyjs file 
 M1  GO LIPID LOCALIZATION   53/1459   5.33E-07  53  2092  298  cyjs file 
 M1  GO LIPID CATABOLIC PROCESS   52/1459   1.59E-07  52  2092  298  cyjs file 
 M2  GO VASCULATURE DEVELOPMENT   50/935   0.001043135  50  1609  338  cyjs file 
 M1  GO ENERGY DERIVATION BY OXIDATION OF ORGANIC COMPOUNDS   49/1459   4.31E-08  49  2092  298  cyjs file 
 M1  GO BLOOD VESSEL MORPHOGENESIS   49/1459   0.018218476  49  2092  298  cyjs file 
 M1  GO REGULATION OF PROTEIN SECRETION   49/1459   0.049833188  49  2092  298  cyjs file 
 M4  GO GENERATION OF PRECURSOR METABOLITES AND ENERGY   49/597   5.35E-18  49  804  62  cyjs file 
 M1  GO LIPID MODIFICATION   43/1459   6.88E-06  43  2092  298  cyjs file 
 M1  GO GLYCEROPHOSPHOLIPID METABOLIC PROCESS   43/1459   0.010221564  43  2092  298  cyjs file 
 M4  GO CELLULAR RESPIRATION   43/597   5.83E-26  43  804  62  cyjs file 
 M1  GO ANGIOGENESIS   42/1459   0.013403466  42  2092  298  cyjs file 
 M1  GO LYTIC VACUOLE MEMBRANE   39/1459   0.020509844  39  2092  298  cyjs file 
 M1  GO VESICLE ORGANIZATION   39/1459   0.026674314  39  2092  298  cyjs file