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Ovary: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Ovary 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

 

 

Notable Pathways:

To facilitate network analysis of the Ovary 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
 M9  GO TRANSLATIONAL INITIATION   99/576   1.06893977285144e-108  99  859  132  cyjs file 
 M9  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   80/576   5.01402004212098e-95  80  859  132  cyjs file 
 M9  GO NUCLEAR TRANSCRIBED MRNA CATABOLIC PROCESS NONSENSE MEDIATED DECAY   81/576   2.02657818680962e-89  81  859  132  cyjs file 
 M9  GO PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   81/576   3.17731055406938e-87  81  859  132  cyjs file 
 M9  GO MULTI ORGANISM METABOLIC PROCESS   84/576   2.92611992353868e-86  84  859  132  cyjs file 
 M9  GO PROTEIN TARGETING TO MEMBRANE   82/576   1.65026709863771e-76  82  859  132  cyjs file 
 M9  GO RRNA METABOLIC PROCESS   93/576   3.09567903250158e-69  93  859  132  cyjs file 
 M9  GO RNA CATABOLIC PROCESS   87/576   9.09019220340537e-67  87  859  132  cyjs file 
 M9  GO CYTOSOLIC PART   86/576   2.6777708626507e-66  86  859  132  cyjs file 
 M9  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO MEMBRANE   91/576   3.16624998608993e-65  91  859  132  cyjs file 
 M9  GO NCRNA PROCESSING   100/576   1.36445271369783e-58  100  859  132  cyjs file 
 M9  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE   96/576   2.89349039277308e-57  96  859  132  cyjs file 
 M9  GO PROTEIN TARGETING   98/576   2.83132601667216e-54  98  859  132  cyjs file 
 M9  GO VIRAL LIFE CYCLE   84/576   4.52818495878968e-53  84  859  132  cyjs file 
 M9  GO PROTEIN LOCALIZATION TO MEMBRANE   92/576   2.43342704456661e-51  92  859  132  cyjs file 
 M9  GO ORGANIC CYCLIC COMPOUND CATABOLIC PROCESS   95/576   3.6627969896888e-49  95  859  132  cyjs file 
 M13  GO ACTIVATION OF IMMUNE RESPONSE   55/270   4.23465793849306e-31  55  336  32  cyjs file 
 M13  GO INFLAMMATORY RESPONSE   52/270   5.86544377453788e-27  52  336  32  cyjs file 
 M13  GO REGULATION OF CELL ACTIVATION   50/270   7.13609055891585e-24  50  336  32  cyjs file 
 M13  GO POSITIVE REGULATION OF CELL ACTIVATION   41/270   2.38175038166218e-23  41  336  32  cyjs file 
 M13  GO ADAPTIVE IMMUNE RESPONSE   39/270   1.21822295106334e-22  39  336  32  cyjs file 
 M13  GO REGULATION OF LEUKOCYTE PROLIFERATION   32/270   3.4053023959283e-20  32  336  32  cyjs file 
 M13  GO IMMUNE RESPONSE REGULATING CELL SURFACE RECEPTOR SIGNALING PATHWAY   38/270   6.32688156981376e-20  38  336  32  cyjs file 
 M13  GO POSITIVE REGULATION OF CELL CELL ADHESION   33/270   4.15210190064116e-19  33  336  32  cyjs file 
 M13  GO IMMUNE EFFECTOR PROCESS   44/270   7.30172676157099e-19  44  336  32  cyjs file