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Muscle: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Muscle 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

 

 

Notable Pathways:

To facilitate network analysis of the Muscle 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 ACTIN FILAMENT BASED PROCESS   77/1390   2.95E-07  77  2252  432  cyjs file 
 M1  GO MUSCLE STRUCTURE DEVELOPMENT   65/1390   0.000453083  65  2252  432  cyjs file 
 M1  GO ACTIN CYTOSKELETON   58/1390   0.02425723  58  2252  432  cyjs file 
 M1  GO MUSCLE SYSTEM PROCESS   56/1390   2.95E-07  56  2252  432  cyjs file 
 M1  GO CONTRACTILE FIBER   54/1390   6.66E-11  54  2252  432  cyjs file 
 M1  GO MUSCLE CONTRACTION   50/1390   2.95E-07  50  2252  432  cyjs file 
 M2  GO ENERGY DERIVATION BY OXIDATION OF ORGANIC COMPOUNDS   47/827   1.50E-15  47  1300  239  cyjs file 
 M1  GO REGULATION OF ACTIN FILAMENT BASED PROCESS   45/1390   0.018188243  45  2252  432  cyjs file 
 M1  GO MUSCLE ORGAN DEVELOPMENT   44/1390   0.003303321  44  2252  432  cyjs file 
 M2  GO PURINE CONTAINING COMPOUND METABOLIC PROCESS   43/827   4.58E-05  43  1300  239  cyjs file 
 M1  GO MUSCLE TISSUE DEVELOPMENT   39/1390   0.038856078  39  2252  432  cyjs file 
 M1  GO MUSCLE CELL DIFFERENTIATION   38/1390   0.009157685  38  2252  432  cyjs file 
 M2  GO NUCLEOSIDE TRIPHOSPHATE METABOLIC PROCESS   36/827   6.30E-08  36  1300  239  cyjs file 
 M2  GO FATTY ACID METABOLIC PROCESS   35/827   7.48E-05  35  1300  239  cyjs file 
 M13  GO POSITIVE REGULATION OF PROTEIN CATABOLIC PROCESS   34/221   1.47E-22  34  305  33  cyjs file 
 M1  GO I BAND   33/1390   2.95E-07  33  2252  432  cyjs file 
 M1  GO REGULATION OF MUSCLE SYSTEM PROCESS   31/1390   0.025836266  31  2252  432  cyjs file 
 M2  GO MITOCHONDRIAL TRANSPORT   30/827   2.72E-07  30  1300  239  cyjs file 
 M2  GO LIPID CATABOLIC PROCESS   30/827   0.000202729  30  1300  239  cyjs file 
 M1  GO STRIATED MUSCLE CELL DIFFERENTIATION   27/1390   0.049752263  27  2252  432  cyjs file 
 M1  GO MUSCLE CELL DEVELOPMENT   26/1390   0.003255581  26  2252  432  cyjs file 
 M1  GO SARCOLEMMA   24/1390   0.010958816  24  2252  432  cyjs file 
 M2  GO MONOCARBOXYLIC ACID CATABOLIC PROCESS   24/827   4.70E-09  24  1300  239  cyjs file 
 M1  GO STRIATED MUSCLE CONTRACTION   22/1390   0.003255581  22  2252  432  cyjs file