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Uterus: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Uterus 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
    M56 module
    M57 module

 

 

Notable Pathways:

To facilitate network analysis of the Uterus 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
 M7  GO TRANSLATIONAL INITIATION   94/420   9.69e-114  94  635  116  cyjs file 
 M7  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   78/420   1.77e-102  78  635  116  cyjs file 
 M7  GO MULTI ORGANISM METABOLIC PROCESS   84/420   1.94e-98  84  635  116  cyjs file 
 M7  GO NUCLEAR TRANSCRIBED MRNA CATABOLIC PROCESS NONSENSE MEDIATED DECAY   79/420   1.87e-97  79  635  116  cyjs file 
 M7  GO PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   79/420   2.81e-95  79  635  116  cyjs file 
 M7  GO PROTEIN TARGETING TO MEMBRANE   78/420   1.04e-81  78  635  116  cyjs file 
 M7  GO RNA CATABOLIC PROCESS   83/420   1.94e-73  83  635  116  cyjs file 
 M7  GO RRNA METABOLIC PROCESS   85/420   2.31e-71  85  635  116  cyjs file 
 M7  GO CYTOSOLIC PART   81/420   2.31e-71  81  635  116  cyjs file 
 M7  GO VIRAL LIFE CYCLE   86/420   2.04e-67  86  635  116  cyjs file 
 M7  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO MEMBRANE   82/420   5.43e-66  82  635  116  cyjs file 
 M7  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE   90/420   2.01e-63  90  635  116  cyjs file 
 M7  GO PROTEIN TARGETING   91/420   8.84e-60  91  635  116  cyjs file 
 M7  GO NCRNA PROCESSING   86/420   4.76e-56  86  635  116  cyjs file 
 M7  GO PROTEIN LOCALIZATION TO MEMBRANE   83/420   1.24e-53  83  635  116  cyjs file 
 M7  GO ORGANIC CYCLIC COMPOUND CATABOLIC PROCESS   87/420   2.62e-53  87  635  116  cyjs file 
 M29  GO ACTIVATION OF IMMUNE RESPONSE   34/148   2.90e-20  34  175  10  cyjs file 
 M7  GO CELL SUBSTRATE JUNCTION   47/420   2.37e-17  47  635  116  cyjs file 
 M7  GO ANCHORING JUNCTION   49/420   3.42e-15  49  635  116  cyjs file 
 M8  GO CELL SUBSTRATE JUNCTION   42/395   4.54e-13  42  596  93  cyjs file 
 M8  GO ANCHORING JUNCTION   45/395   3.10e-12  45  596  93  cyjs file 
 M8  GO ACTIN CYTOSKELETON   37/395   7.20e-09  37  596  93  cyjs file 
 M8  GO ACTIN BINDING   31/395   7.17e-07  31  596  93  cyjs file 
 M7  GO POSTTRANSCRIPTIONAL REGULATION OF GENE EXPRESSION   32/420   3.92e-06  32  635  116  cyjs file 
 M8  GO ACTIN FILAMENT BASED PROCESS   31/395   1.32e-05  31  596  93  cyjs file