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Blood: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Blood 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

 

 

Notable Pathways:

To facilitate network analysis of the Blood 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
 M1  GO CELL DIVISION   203/4455   3.17E-15  203  6344  756  cyjs file 
 M1  GO NEGATIVE REGULATION OF CELL CYCLE   159/4455   1.33E-05  159  6344  756  cyjs file 
 M1  GO REGULATION OF CELL CYCLE PHASE TRANSITION   149/4455   2.97E-13  149  6344  756  cyjs file 
 M1  GO AUTOPHAGY   128/4455   0.019505431  128  6344  756  cyjs file 
 M1  GO SPINDLE   123/4455   3.94E-08  123  6344  756  cyjs file 
 M1  GO DNA REPLICATION   117/4455   5.31E-18  117  6344  756  cyjs file 
 M1  GO COFACTOR METABOLIC PROCESS   113/4455   0.009074645  113  6344  756  cyjs file 
 M1  GO REGULATION OF MICROTUBULE BASED PROCESS   105/4455   2.14E-07  105  6344  756  cyjs file 
 M1  GO REGULATION OF CELLULAR PROTEIN CATABOLIC PROCESS   105/4455   0.000105825  105  6344  756  cyjs file 
 M1  GO CELL CYCLE CHECKPOINT   99/4455   8.39E-12  99  6344  756  cyjs file 
 M1  GO MACROAUTOPHAGY   93/4455   0.034346928  93  6344  756  cyjs file 
 M1  GO REGULATION OF CELL DIVISION   92/4455   0.020526429  92  6344  756  cyjs file 
 M1  GO REGULATION OF GENE EXPRESSION EPIGENETIC   87/4455   0.000699987  87  6344  756  cyjs file 
 M1  GO MITOCHONDRIAL TRANSPORT   82/4455   2.21E-07  82  6344  756  cyjs file 
 M1  GO MITOTIC CELL CYCLE CHECKPOINT   72/4455   5.73E-09  72  6344  756  cyjs file 
 M1  GO CELL CYCLE G2 M PHASE TRANSITION   59/4455   0.000269743  59  6344  756  cyjs file 
 M1  GO PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   58/4455   1.07E-05  58  6344  756  cyjs file 
 M1  GO REGULATION OF PROTEASOMAL UBIQUITIN DEPENDENT PROTEIN CATABOLIC PROCESS   58/4455   0.003815832  58  6344  756  cyjs file 
 M1  GO CHROMATIN REMODELING   57/4455   0.008818274  57  6344  756  cyjs file 
 M1  GO MICROTUBULE ORGANIZING CENTER PART   55/4455   0.01069416  55  6344  756  cyjs file 
 M1  GO SIGNAL TRANSDUCTION BY P53 CLASS MEDIATOR   54/4455   0.000629226  54  6344  756  cyjs file 
 M1  GO RESPONSE TO IONIZING RADIATION   54/4455   0.016697294  54  6344  756  cyjs file 
 M1  GO INTRINSIC APOPTOTIC SIGNALING PATHWAY   54/4455   0.041050444  54  6344  756  cyjs file 
 M1  GO POSITIVE REGULATION OF MITOTIC CELL CYCLE   52/4455   0.000965814  52  6344  756  cyjs file