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Salivary_Gland: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Salivary_Gland 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



Notable Pathways:

To facilitate network analysis of the Salivary_Gland 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
 M23  GO TRANSLATIONAL INITIATION   70/125   3.53311445766508e-115  70  168  22  cyjs file 
 M23  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   64/125   2.28889134530857e-114  64  168  22  cyjs file 
 M23  GO NUCLEAR TRANSCRIBED MRNA CATABOLIC PROCESS NONSENSE MEDIATED DECAY   64/125   1.75093020345935e-109  64  168  22  cyjs file 
 M23  GO MULTI ORGANISM METABOLIC PROCESS   66/125   2.16701878341927e-108  66  168  22  cyjs file 
 M23  GO PROTEIN LOCALIZATION TO ENDOPLASMIC RETICULUM   64/125   4.94947867671818e-108  64  168  22  cyjs file 
 M23  GO PROTEIN TARGETING TO MEMBRANE   64/125   3.80957565634138e-99  64  168  22  cyjs file 
 M23  GO RNA CATABOLIC PROCESS   65/125   6.24277449096583e-89  65  168  22  cyjs file 
 M23  GO CYTOSOLIC PART   64/125   1.67960524700976e-87  64  168  22  cyjs file 
 M23  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO MEMBRANE   66/125   4.38759289416339e-86  66  168  22  cyjs file 
 M23  GO RRNA METABOLIC PROCESS   65/125   2.92922598013353e-85  65  168  22  cyjs file 
 M23  GO VIRAL LIFE CYCLE   66/125   4.08111252669821e-83  66  168  22  cyjs file 
 M19  GO OXIDATIVE PHOSPHORYLATION   51/181   6.1190369318988e-79  51  230  17  cyjs file 
 M19  GO CELLULAR RESPIRATION   59/181   1.01319222405192e-78  59  230  17  cyjs file 
 M23  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE   67/125   4.23809783893113e-78  67  168  22  cyjs file 
 M23  GO PROTEIN LOCALIZATION TO MEMBRANE   67/125   7.70784063176279e-77  67  168  22  cyjs file 
 M23  GO PROTEIN TARGETING   67/125   1.84937393598305e-74  67  168  22  cyjs file 
 M23  GO NCRNA PROCESSING   66/125   2.75083579861262e-74  66  168  22  cyjs file 
 M19  GO ELECTRON TRANSPORT CHAIN   50/181   1.99958914419965e-73  50  230  17  cyjs file 
 M23  GO ORGANIC CYCLIC COMPOUND CATABOLIC PROCESS   66/125   3.10139217912233e-71  66  168  22  cyjs file 
 M19  GO GENERATION OF PRECURSOR METABOLITES AND ENERGY   67/181   1.70279027229773e-70  67  230  17  cyjs file 
 M19  GO NUCLEOSIDE TRIPHOSPHATE METABOLIC PROCESS   62/181   6.4465764281337e-70  62  230  17  cyjs file 
 M19  GO ENERGY DERIVATION BY OXIDATION OF ORGANIC COMPOUNDS   61/181   9.5403364002454e-70  61  230  17  cyjs file 
 M19  GO RESPIRATORY CHAIN   45/181   1.83204499810566e-67  45  230  17  cyjs file 
 M19  GO NUCLEOSIDE MONOPHOSPHATE METABOLIC PROCESS   61/181   6.24776727847336e-67  61  230  17  cyjs file 
 M19  GO GLYCOSYL COMPOUND METABOLIC PROCESS   62/181   5.1242958884086e-56  62  230  17  cyjs file