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Testis: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Testis 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

 

 

Notable Pathways:

To facilitate network analysis of the Testis 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
 M3  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   77/1944   2.83e-47  77  2820  406  cyjs file 
 M3  GO NUCLEAR TRANSCRIBED MRNA CATABOLIC PROCESS NONSENSE MEDIATED DECAY   80/1944   1.36e-44  80  2820  406  cyjs file 
 M3  GO TRANSLATIONAL INITIATION   89/1944   3.66e-44  89  2820  406  cyjs file 
 M3  GO PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   81/1944   6.72e-44  81  2820  406  cyjs file 
 M3  GO MULTI ORGANISM METABOLIC PROCESS   81/1944   1.98e-38  81  2820  406  cyjs file 
 M3  GO PROTEIN TARGETING TO MEMBRANE   86/1944   1.04e-37  86  2820  406  cyjs file 
 M3  GO CYTOSOLIC PART   95/1944   2.65e-30  95  2820  406  cyjs file 
 M3  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO MEMBRANE   102/1944   2.24e-28  102  2820  406  cyjs file 
 M3  GO CELL SUBSTRATE JUNCTION   129/1944   2.10e-27  129  2820  406  cyjs file 
 M3  GO RNA CATABOLIC PROCESS   91/1944   1.18e-26  91  2820  406  cyjs file 
 M3  GO PROTEIN LOCALIZATION TO MEMBRANE   122/1944   6.10e-26  122  2820  406  cyjs file 
 M3  GO BLOOD VESSEL MORPHOGENESIS   119/1944   1.25e-25  119  2820  406  cyjs file 
 M3  GO VIRAL LIFE CYCLE   102/1944   1.12e-24  102  2820  406  cyjs file 
 M3  GO VASCULATURE DEVELOPMENT   137/1944   2.74e-24  137  2820  406  cyjs file 
 M3  GO ANCHORING JUNCTION   140/1944   6.43e-24  140  2820  406  cyjs file 
 M3  GO EXTRACELLULAR STRUCTURE ORGANIZATION   102/1944   6.53e-23  102  2820  406  cyjs file 
 M3  GO ANGIOGENESIS   97/1944   2.92e-21  97  2820  406  cyjs file 
 M3  GO ORGANIC CYCLIC COMPOUND CATABOLIC PROCESS   121/1944   3.67e-20  121  2820  406  cyjs file 
 M3  GO RRNA METABOLIC PROCESS   86/1944   2.09e-19  86  2820  406  cyjs file 
 M3  GO EXTRACELLULAR MATRIX   119/1944   2.71e-19  119  2820  406  cyjs file 
 M3  GO PROTEIN TARGETING   114/1944   1.20e-18  114  2820  406  cyjs file 
 M3  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE   105/1944   2.36e-18  105  2820  406  cyjs file 
 M3  GO PROTEINACEOUS EXTRACELLULAR MATRIX   97/1944   8.28e-15  97  2820  406  cyjs file 
 M3  GO POSITIVE REGULATION OF LOCOMOTION   105/1944   2.65e-13  105  2820  406  cyjs file 
 M3  GO SKELETAL SYSTEM DEVELOPMENT   110/1944   6.63e-13  110  2820  406  cyjs file