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Heart: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Heart 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
    M45 module
    M46 module
    M47 module
    M48 module
    M49 module
    M50 module
    M51 module
    M52 module
    M53 module
    M54 module
    M55 module
    M56 module
    M57 module
    M58 module
    M59 module
    M60 module
    M61 module

 

 

Notable Pathways:

To facilitate network analysis of the Heart 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 UBIQUITIN LIKE PROTEIN TRANSFERASE ACTIVITY   100/2288   1.65E-05  100  3532  595  cyjs file 
 M1  GO CENTROSOME   95/2288   0.013254046  95  3532  595  cyjs file 
 M1  GO ACTIN FILAMENT BASED PROCESS   94/2288   0.002953805  94  3532  595  cyjs file 
 M1  GO HEART DEVELOPMENT   93/2288   0.00799393  93  3532  595  cyjs file 
 M1  GO MITOCHONDRIAL MATRIX   92/2288   0.00041887  92  3532  595  cyjs file 
 M1  GO ANCHORING JUNCTION   92/2288   0.031055272  92  3532  595  cyjs file 
 M1  GO CONTRACTILE FIBER   47/2288   0.023278061  47  3532  595  cyjs file 
 M1  GO CARDIAC MUSCLE TISSUE DEVELOPMENT   35/2288   0.017309839  35  3532  595  cyjs file 
 M1  GO EARLY ENDOSOME MEMBRANE   29/2288   0.028977516  29  3532  595  cyjs file 
 M1  GO REGULATION OF HEART RATE   25/2288   0.014992234  25  3532  595  cyjs file 
 M1  GO CARDIAC CONDUCTION   24/2288   0.015872286  24  3532  595  cyjs file 
 M1  GO CARDIAC MUSCLE CELL DIFFERENTIATION   22/2288   0.018940808  22  3532  595  cyjs file 
 M1  GO FATTY ACID CATABOLIC PROCESS   21/2288   0.03295819  21  3532  595  cyjs file 
 M2  GO MITOCHONDRIAL MATRIX   74/1195   1.61E-10  74  1955  428  cyjs file 
 M2  GO HEART DEVELOPMENT   54/1195   0.014366356  54  1955  428  cyjs file 
 M2  GO FATTY ACID METABOLIC PROCESS   44/1195   0.000258358  44  1955  428  cyjs file 
 M2  GO LIPID CATABOLIC PROCESS   41/1195   4.85E-05  41  1955  428  cyjs file 
 M2  GO CELLULAR LIPID CATABOLIC PROCESS   34/1195   7.21E-07  34  1955  428  cyjs file 
 M2  GO MONOSACCHARIDE METABOLIC PROCESS   34/1195   0.0002507  34  1955  428  cyjs file 
 M2  GO HEXOSE METABOLIC PROCESS   30/1195   9.03E-05  30  1955  428  cyjs file 
 M2  GO CELLULAR RESPIRATION   28/1195   0.000112574  28  1955  428  cyjs file 
 M2  GO FATTY ACID CATABOLIC PROCESS   22/1195   1.61E-06  22  1955  428  cyjs file 
 M3  GO REGULATION OF MICROTUBULE BASED PROCESS   22/638   0.043343423  22  1013  177  cyjs file 
 M4  GO MITOCHONDRIAL MEMBRANE PART   60/376   3.19E-53  60  534  55  cyjs file