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Liver: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Liver 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
    M62 module
    M63 module
    M64 module
    M65 module
    M66 module
    M67 module
    M68 module
    M69 module



Notable Pathways:

To facilitate network analysis of the Liver 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 REGULATION OF CELLULAR AMIDE METABOLIC PROCESS   58/1152   6.35E-08  58  1720  271  cyjs file 
 M1  GO REGULATION OF MITOTIC CELL CYCLE   52/1152   0.012015429  52  1720  271  cyjs file 
 M31  GO GLYCOSYL COMPOUND METABOLIC PROCESS   49/124   1.68E-47  49  153  11  cyjs file 
 M1  GO RIBOSOME BIOGENESIS   46/1152   3.98E-05  46  1720  271  cyjs file 
 M9  GO SMALL MOLECULE CATABOLIC PROCESS   46/377   7.94E-21  46  540  80  cyjs file 
 M3  GO CELL SUBSTRATE JUNCTION   45/808   2.91E-05  45  1130  121  cyjs file 
 M3  GO RESPONSE TO GROWTH FACTOR   45/808   0.00118594  45  1130  121  cyjs file 
 M31  GO MITOCHONDRIAL PROTEIN COMPLEX   43/124   2.60E-58  43  153  11  cyjs file 
 M50  GO MULTI ORGANISM METABOLIC PROCESS   43/61   1.25E-76  43  79  7  cyjs file 
 M50  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE   43/61   2.48E-57  43  79  7  cyjs file 
 M31  GO INNER MITOCHONDRIAL MEMBRANE PROTEIN COMPLEX   42/124   2.28E-61  42  153  11  cyjs file 
 M50  GO PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   42/61   1.25E-76  42  79  7  cyjs file 
 M50  GO PROTEIN TARGETING TO MEMBRANE   42/61   1.44E-71  42  79  7  cyjs file 
 M2  GO REGULATION OF PROTEIN CATABOLIC PROCESS   41/737   2.06E-05  41  1230  248  cyjs file 
 M31  GO GENERATION OF PRECURSOR METABOLITES AND ENERGY   41/124   4.29E-40  41  153  11  cyjs file 
 M31  GO CELLULAR RESPIRATION   39/124   4.93E-50  39  153  11  cyjs file 
 M9  GO CELLULAR AMINO ACID METABOLIC PROCESS   38/377   5.36E-14  38  540  80  cyjs file 
 M2  GO POSITIVE REGULATION OF CATABOLIC PROCESS   37/737   0.000602395  37  1230  248  cyjs file 
 M3  GO REGULATION OF HOMEOSTATIC PROCESS   36/808   0.031869954  36  1130  121  cyjs file 
 M9  GO MITOCHONDRIAL MATRIX   36/377   4.79E-10  36  540  80  cyjs file 
 M3  GO REGULATION OF PROTEIN SECRETION   34/808   0.016341545  34  1130  121  cyjs file 
 M9  GO COFACTOR BINDING   34/377   5.36E-14  34  540  80  cyjs file 
 M2  GO ACTIVATION OF IMMUNE RESPONSE   32/737   0.048249293  32  1230  248  cyjs file 
 M9  GO FATTY ACID METABOLIC PROCESS   30/377   7.45E-10  30  540  80  cyjs file