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Kidney: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Kidney 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

 

 

Notable Pathways:

To facilitate network analysis of the Kidney 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 CELL ACTIVATION   143/2130   1.30E-20  143  3139  468  cyjs file 
 M1  GO REGULATION OF CELL CELL ADHESION   117/2130   1.35E-18  117  3139  468  cyjs file 
 M1  GO SIDE OF MEMBRANE   108/2130   6.56E-11  108  3139  468  cyjs file 
 M1  GO REGULATION OF HOMEOSTATIC PROCESS   84/2130   0.002023152  84  3139  468  cyjs file 
 M2  GO PURINE CONTAINING COMPOUND METABOLIC PROCESS   75/1245   1.92E-12  75  2044  368  cyjs file 
 M1  GO REGULATION OF PROTEIN CATABOLIC PROCESS   71/2130   0.014528607  71  3139  468  cyjs file 
 M4  GO CELLULAR AMINO ACID METABOLIC PROCESS   64/652   1.51E-24  64  989  176  cyjs file 
 M1  GO NEGATIVE REGULATION OF CELL ADHESION   62/2130   7.04E-08  62  3139  468  cyjs file 
 M1  GO ORGANELLE SUBCOMPARTMENT   62/2130   0.003004712  62  3139  468  cyjs file 
 M1  GO ENDOCYTIC VESICLE   51/2130   0.009310374  51  3139  468  cyjs file 
 M1  GO EXTERNAL SIDE OF PLASMA MEMBRANE   49/2130   0.006010623  49  3139  468  cyjs file 
 M1  GO EXTRINSIC COMPONENT OF MEMBRANE   49/2130   0.017225874  49  3139  468  cyjs file 
 M1  GO POSITIVE REGULATION OF HEMOPOIESIS   47/2130   1.65E-06  47  3139  468  cyjs file 
 M8  GO ORGANIC ANION TRANSPORT   37/519   1.92E-07  37  740  86  cyjs file 
 M1  GO NEGATIVE REGULATION OF HOMOTYPIC CELL CELL ADHESION   36/2130   2.72E-07  36  3139  468  cyjs file 
 M3  GO CILIUM   36/447   2.58E-05  36  999  357  cyjs file 
 M2  GO HYDROGEN TRANSPORT   35/1245   9.09E-09  35  2044  368  cyjs file 
 M4  GO ALCOHOL METABOLIC PROCESS   35/652   1.23E-05  35  989  176  cyjs file 
 M6  GO SMALL MOLECULE BIOSYNTHETIC PROCESS   35/496   1.62E-05  35  772  142  cyjs file 
 M8  GO MONOVALENT INORGANIC CATION TRANSPORT   35/519   2.04E-05  35  740  86  cyjs file 
 M6  GO GLYCOSYL COMPOUND METABOLIC PROCESS   27/496   0.000875387  27  772  142  cyjs file 
 M14  GO MORPHOGENESIS OF AN EPITHELIUM   22/260   8.59E-05  22  470  113  cyjs file 
 M1  GO ERYTHROCYTE HOMEOSTASIS   19/2130   0.02067378  19  3139  468  cyjs file 
 M23  GO CELLULAR AMINO ACID METABOLIC PROCESS   13/210   0.011555131  13  252  15  cyjs file