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Pituitary: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Pituitary 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



Notable Pathways:

To facilitate network analysis of the Pituitary 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 CYTOSOLIC RIBOSOME   78/215   5.15E-124  78  305  45  cyjs file 
 M16  GO CYTOSOLIC PART   78/215   7.07E-93  78  305  45  cyjs file 
 M16  GO PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   77/215   1.98E-117  77  305  45  cyjs file 
 M16  GO PROTEIN TARGETING TO MEMBRANE   77/215   7.84E-106  77  305  45  cyjs file 
 M3  GO AXON   71/781   1.17E-18  71  1234  225  cyjs file 
 M3  GO SYNAPTIC SIGNALING   71/781   1.37E-18  71  1234  225  cyjs file 
 M3  GO SECRETION BY CELL   51/781   2.20E-06  51  1234  225  cyjs file 
 M3  GO MODULATION OF SYNAPTIC TRANSMISSION   50/781   7.47E-13  50  1234  225  cyjs file 
 M3  GO TRANSPORTER COMPLEX   50/781   7.54E-12  50  1234  225  cyjs file 
 M16  GO CELL SUBSTRATE JUNCTION   41/215   4.07E-24  41  305  45  cyjs file 
 M16  GO ANCHORING JUNCTION   41/215   1.02E-20  41  305  45  cyjs file 
 M2  GO REGULATION OF PROTEIN CATABOLIC PROCESS   41/933   0.00264334  41  1340  201  cyjs file 
 M2  GO NEGATIVE REGULATION OF INTRACELLULAR SIGNAL TRANSDUCTION   41/933   0.013570699  41  1340  201  cyjs file 
 M2  GO REGULATION OF CYTOPLASMIC TRANSPORT   41/933   0.049463188  41  1340  201  cyjs file 
 M3  GO PROTEIN SERINE THREONINE KINASE ACTIVITY   40/781   0.001054127  40  1234  225  cyjs file 
 M3  GO REGULATION OF VESICLE MEDIATED TRANSPORT   40/781   0.00207236  40  1234  225  cyjs file 
 M3  GO POSITIVE REGULATION OF CELL DEVELOPMENT   40/781   0.003085246  40  1234  225  cyjs file 
 M6  GO POSITIVE REGULATION OF PROTEOLYSIS   38/696   9.07E-06  38  1001  132  cyjs file 
 M6  GO REGULATION OF PROTEIN CATABOLIC PROCESS   38/696   5.35E-05  38  1001  132  cyjs file 
 M3  GO REGULATION OF CYTOPLASMIC TRANSPORT   36/781   0.032294327  36  1234  225  cyjs file 
 M3  GO EXOCYTOSIS   35/781   3.92E-05  35  1234  225  cyjs file 
 M3  GO GLYCOSYL COMPOUND METABOLIC PROCESS   35/781   0.001037005  35  1234  225  cyjs file 
 M12  GO EXTRACELLULAR MATRIX   34/343   6.35E-09  34  454  63  cyjs file