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Brain: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Brain 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



Notable Pathways:

To facilitate network analysis of the Brain 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
 M2  GO ENDOSOMAL PART   59/1211   0.000446855  59  1924  384  cyjs file 
 M2  GO MICROTUBULE   50/1211   0.010512599  50  1924  384  cyjs file 
 M18  GO CELL SUBSTRATE JUNCTION   44/250   2.19E-24  44  355  52  cyjs file 
 M2  GO EARLY ENDOSOME   40/1211   0.010512599  40  1924  384  cyjs file 
 M2  GO NEGATIVE REGULATION OF NERVOUS SYSTEM DEVELOPMENT   38/1211   0.004206439  38  1924  384  cyjs file 
 M2  GO LATE ENDOSOME   32/1211   0.006660352  32  1924  384  cyjs file 
 M2  GO REGULATION OF MICROTUBULE BASED PROCESS   32/1211   0.036375914  32  1924  384  cyjs file 
 M22  GO CELLULAR RESPIRATION   31/156   6.30E-32  31  217  21  cyjs file 
 M11  GO NEGATIVE REGULATION OF INTRACELLULAR SIGNAL TRANSDUCTION   30/409   1.24E-05  30  523  51  cyjs file 
 M12  GO SYNAPTIC SIGNALING   30/276   2.81E-08  30  486  135  cyjs file 
 M22  GO RESPIRATORY CHAIN   28/156   3.58E-35  28  217  21  cyjs file 
 M5  GO FOREBRAIN DEVELOPMENT   28/538   0.000589475  28  788  145  cyjs file 
 M5  GO RESPONSE TO GROWTH FACTOR   28/538   0.017004914  28  788  145  cyjs file 
 M5  GO REGULATION OF NEURON PROJECTION DEVELOPMENT   27/538   0.006478086  27  788  145  cyjs file 
 M2  GO ENSHEATHMENT OF NEURONS   25/1211   1.06E-05  25  1924  384  cyjs file 
 M2  GO REGULATION OF AXONOGENESIS   25/1211   0.028155587  25  1924  384  cyjs file 
 M5  GO POSITIVE REGULATION OF NERVOUS SYSTEM DEVELOPMENT   25/538   0.032970159  25  788  145  cyjs file 
 M6  GO PRESYNAPSE   25/505   0.001812135  25  732  105  cyjs file 
 M8  GO SYNAPTIC SIGNALING   25/396   0.015468719  25  608  111  cyjs file 
 M5  GO NEURON PROJECTION MORPHOGENESIS   24/538   0.025720911  24  788  145  cyjs file 
 M5  GO CELL MORPHOGENESIS INVOLVED IN NEURON DIFFERENTIATION   23/538   0.019665803  23  788  145  cyjs file 
 M2  GO RECYCLING ENDOSOME   21/1211   0.028204915  21  1924  384  cyjs file 
 M12  GO POSTSYNAPSE   19/276   0.00092719  19  486  135  cyjs file