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Spleen: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Spleen 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
    M46 module
    M47 module
    M48 module
    M49 module
    M50 module
    M51 module
    M52 module
    M53 module
    M54 module
    M55 module



Notable Pathways:

To facilitate network analysis of the Spleen 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
 M21  GO TRANSLATIONAL INITIATION   85/219   2.33E-125  85  339  70  cyjs file 
 M21  GO MULTI ORGANISM METABOLIC PROCESS   81/219   1.65E-119  81  339  70  cyjs file 
 M21  GO PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   78/219   8.21E-119  78  339  70  cyjs file 
 M21  GO PROTEIN TARGETING TO MEMBRANE   78/219   6.01E-107  78  339  70  cyjs file 
 M21  GO RNA CATABOLIC PROCESS   80/219   7.79E-95  80  339  70  cyjs file 
 M21  GO CYTOSOLIC PART   79/219   8.50E-94  79  339  70  cyjs file 
 M21  GO RRNA METABOLIC PROCESS   81/219   7.50E-92  81  339  70  cyjs file 
 M21  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO MEMBRANE   79/219   4.75E-87  79  339  70  cyjs file 
 M21  GO VIRAL LIFE CYCLE   81/219   1.05E-86  81  339  70  cyjs file 
 M21  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE   82/219   1.07E-79  82  339  70  cyjs file 
 M21  GO NCRNA PROCESSING   83/219   1.16E-78  83  339  70  cyjs file 
 M21  GO PROTEIN TARGETING   82/219   3.19E-75  82  339  70  cyjs file 
 M21  GO PROTEIN LOCALIZATION TO MEMBRANE   80/219   3.66E-75  80  339  70  cyjs file 
 M21  GO ORGANIC CYCLIC COMPOUND CATABOLIC PROCESS   83/219   8.39E-75  83  339  70  cyjs file 
 M12  GO ORGANELLE FISSION   93/334   1.28E-62  93  491  81  cyjs file 
 M12  GO CELL DIVISION   90/334   2.85E-62  90  491  81  cyjs file 
 M12  GO CHROMOSOME SEGREGATION   72/334   6.14E-59  72  491  81  cyjs file 
 M12  GO SISTER CHROMATID SEGREGATION   58/334   4.60E-53  58  491  81  cyjs file 
 M12  GO NUCLEAR CHROMOSOME SEGREGATION   63/334   1.53E-52  63  491  81  cyjs file 
 M12  GO CHROMOSOMAL REGION   66/334   2.34E-45  66  491  81  cyjs file 
 M12  GO CHROMOSOME CENTROMERIC REGION   51/334   1.50E-43  51  491  81  cyjs file 
 M12  GO DNA REPLICATION   53/334   7.54E-42  53  491  81  cyjs file 
 M12  GO CELL CYCLE PHASE TRANSITION   57/334   8.92E-42  57  491  81  cyjs file