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Vagina: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Vagina 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

 

 

Notable Pathways:

To facilitate network analysis of the Vagina 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
 M16  GO NUCLEOSIDE TRIPHOSPHATE METABOLIC PROCESS   54/246   4.16e-48  54  314  31  cyjs file 
 M16  GO OXIDATIVE PHOSPHORYLATION   38/246   1.10e-45  38  314  31  cyjs file 
 M16  GO NUCLEOSIDE MONOPHOSPHATE METABOLIC PROCESS   53/246   1.10e-45  53  314  31  cyjs file 
 M16  GO ELECTRON TRANSPORT CHAIN   39/246   3.37e-45  39  314  31  cyjs file 
 M16  GO CELLULAR RESPIRATION   44/246   1.65e-44  44  314  31  cyjs file 
 M16  GO RESPIRATORY CHAIN   36/246   2.79e-43  36  314  31  cyjs file 
 M16  GO PURINE CONTAINING COMPOUND METABOLIC PROCESS   58/246   8.04e-40  58  314  31  cyjs file 
 M16  GO GLYCOSYL COMPOUND METABOLIC PROCESS   56/246   3.49e-39  56  314  31  cyjs file 
 M18  GO NCRNA PROCESSING   51/182   9.42e-39  51  228  14  cyjs file 
 M16  GO ENERGY DERIVATION BY OXIDATION OF ORGANIC COMPOUNDS   44/246   6.60e-36  44  314  31  cyjs file 
 M16  GO GENERATION OF PRECURSOR METABOLITES AND ENERGY   47/246   1.15e-33  47  314  31  cyjs file 
 M18  GO RRNA METABOLIC PROCESS   40/182   6.18e-33  40  228  14  cyjs file 
 M31  GO LYMPHOCYTE ACTIVATION   31/102   2.11e-25  31  140  23  cyjs file 
 M31  GO LEUKOCYTE ACTIVATION   32/102   1.92e-24  32  140  23  cyjs file 
 M16  GO CELLULAR PROTEIN COMPLEX ASSEMBLY   36/246   5.09e-19  36  314  31  cyjs file 
 M5  GO NUCLEAR BODY   40/523   1.99e-09  40  783  99  cyjs file 
 M9  GO ANCHORING JUNCTION   33/301   1.53e-08  33  464  85  cyjs file 
 M6  GO POSTTRANSCRIPTIONAL REGULATION OF GENE EXPRESSION   35/410   1.37e-07  35  637  104  cyjs file 
 M5  GO MRNA PROCESSING   39/523   7.51e-07  39  783  99  cyjs file 
 M1  GO REGULATION OF SMALL GTPASE MEDIATED SIGNAL TRANSDUCTION   92/3047   2.31e-06  92  5034  1043  cyjs file 
 M1  GO VASCULATURE DEVELOPMENT   136/3047   2.88e-06  136  5034  1043  cyjs file 
 M5  GO RNA SPLICING   34/523   3.16e-06  34  783  99  cyjs file 
 M2  GO SKIN DEVELOPMENT   37/1004   3.98e-06  37  1576  281  cyjs file 
 M5  GO REGULATION OF SEQUENCE SPECIFIC DNA BINDING TRANSCRIPTION FACTOR ACTIVITY   33/523   7.30e-06  33  783  99  cyjs file 
 M5  GO REGULATION OF PROTEIN SERINE THREONINE KINASE ACTIVITY   38/523   1.13e-05  38  783  99  cyjs file