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Blood_Vessel: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Blood_Vessel 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

 

 

Notable Pathways:

To facilitate network analysis of the Blood_Vessel 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 ACTIVATION OF IMMUNE RESPONSE   101/972   1.69E-32  101  1314  154  cyjs file 
 M3  GO IMMUNE EFFECTOR PROCESS   94/972   1.54E-23  94  1314  154  cyjs file 
 M9  GO PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   79/332   3.96E-104  79  531  107  cyjs file 
 M1  GO UBIQUITIN LIKE PROTEIN TRANSFERASE ACTIVITY   73/1176   5.69E-10  73  1686  226  cyjs file 
 M3  GO LYMPHOCYTE ACTIVATION   73/972   1.11E-20  73  1314  154  cyjs file 
 M3  GO POSITIVE REGULATION OF CYTOKINE PRODUCTION   72/972   3.71E-18  72  1314  154  cyjs file 
 M3  GO CYTOKINE MEDIATED SIGNALING PATHWAY   72/972   1.34E-13  72  1314  154  cyjs file 
 M3  GO ADAPTIVE IMMUNE RESPONSE   71/972   9.37E-24  71  1314  154  cyjs file 
 M3  GO POSITIVE REGULATION OF DEFENSE RESPONSE   71/972   5.63E-18  71  1314  154  cyjs file 
 M3  GO LEUKOCYTE CELL CELL ADHESION   63/972   3.73E-21  63  1314  154  cyjs file 
 M3  GO REGULATION OF HOMOTYPIC CELL CELL ADHESION   63/972   4.73E-17  63  1314  154  cyjs file 
 M3  GO POSITIVE REGULATION OF CELL ADHESION   62/972   2.32E-12  62  1314  154  cyjs file 
 M3  GO REGULATION OF RESPONSE TO WOUNDING   62/972   1.26E-10  62  1314  154  cyjs file 
 M3  GO POSITIVE REGULATION OF CELL CELL ADHESION   53/972   1.83E-15  53  1314  154  cyjs file 
 M3  GO REGULATION OF VESICLE MEDIATED TRANSPORT   53/972   1.82E-05  53  1314  154  cyjs file 
 M3  GO LYTIC VACUOLE MEMBRANE   50/972   1.58E-11  50  1314  154  cyjs file 
 M6  GO BLOOD VESSEL MORPHOGENESIS   48/504   2.33E-15  48  695  85  cyjs file 
 M4  GO VASCULATURE DEVELOPMENT   45/690   7.81E-05  45  1089  219  cyjs file 
 M1  GO MICROTUBULE CYTOSKELETON ORGANIZATION   43/1176   0.01023354  43  1686  226  cyjs file 
 M6  GO ANGIOGENESIS   43/504   2.33E-15  43  695  85  cyjs file 
 M3  GO WOUND HEALING   42/972   0.017937959  42  1314  154  cyjs file 
 M9  GO ANCHORING JUNCTION   41/332   1.64E-13  41  531  107  cyjs file 
 M15  GO EXTRACELLULAR MATRIX   40/251   1.07E-17  40  358  54  cyjs file 
 M4  GO ANCHORING JUNCTION   40/690   0.004310794  40  1089  219  cyjs file