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Nerve: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Nerve 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

 

 

Notable Pathways:

To facilitate network analysis of the Nerve 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
 M12  GO GLIOGENESIS   22/835   0.013954164  22  996  735  cyjs file 
 M13  GO CELL MORPHOGENESIS INVOLVED IN NEURON DIFFERENTIATION   25/383   7.34E-05  25  455  241  cyjs file 
 M13  GO NEURON PROJECTION MORPHOGENESIS   25/383   0.000264656  25  455  241  cyjs file 
 M13  GO FOREBRAIN DEVELOPMENT   18/383   0.022176364  18  455  241  cyjs file 
 M28  GO ENDOSOMAL PART   50/817   2.11E-05  50  973  208  cyjs file 
 M28  GO ENDOMEMBRANE SYSTEM ORGANIZATION   44/817   0.00285097  44  973  208  cyjs file 
 M28  GO GOLGI VESICLE TRANSPORT   34/817   0.002820057  34  973  208  cyjs file 
 M28  GO EARLY ENDOSOME   29/817   0.036480527  29  973  208  cyjs file 
 M28  GO VESICLE ORGANIZATION   28/817   0.026829653  28  973  208  cyjs file 
 M28  GO LATE ENDOSOME   26/817   0.002820057  26  973  208  cyjs file 
 M3  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   83/1238   1.95E-72  83  1494  935  cyjs file 
 M3  GO MITOCHONDRIAL PROTEIN COMPLEX   75/1238   3.07E-47  75  1494  935  cyjs file 
 M3  GO CELLULAR RESPIRATION   63/1238   3.72E-32  63  1494  935  cyjs file 
 M3  GO REGULATION OF PROTEIN CATABOLIC PROCESS   58/1238   5.66E-06  58  1494  935  cyjs file 
 M3  GO POSITIVE REGULATION OF CATABOLIC PROCESS   46/1238   0.016848948  46  1494  935  cyjs file 
 M3  GO MITOCHONDRIAL TRANSPORT   42/1238   2.34E-10  42  1494  935  cyjs file 
 M3  GO MYELIN SHEATH   28/1238   0.000706268  28  1494  935  cyjs file 
 M3  GO NEGATIVE REGULATION OF CANONICAL WNT SIGNALING PATHWAY   27/1238   0.000945677  27  1494  935  cyjs file 
 M34  GO POSITIVE REGULATION OF CELL PROJECTION ORGANIZATION   20/235   4.37E-06  20  281  169  cyjs file 
 M34  GO POSITIVE REGULATION OF NEURON DIFFERENTIATION   20/235   4.37E-06  20  281  169  cyjs file 
 M34  GO TAXIS   20/235   0.001176651  20  281  169  cyjs file 
 M34  GO AXON   18/235   0.002122839  18  281  169  cyjs file 
 M4  GO AXON   22/259   0.000169346  22  309  132  cyjs file 
 M4  GO REGULATION OF NEURON PROJECTION DEVELOPMENT   19/259   0.003846117  19  309  132  cyjs file