Functional Gene Networks

Functional enrichment with DAVID

Server: http://david.abcc.ncifcrf.gov/summary.jsp

Formatted results from functional enrichment and clustering: DAVID_formatted.txt

Arguments set for the query:
Genes: (1) 627
geneIdType: ENTREZ_GENE_ID
geneLabels: geneListSymbol
annotations: c, GOTERM_BP_ALL, GOTERM_MF_ALL, GOTERM_CC_ALL, KEGG_PATHWAY, INTERPRO
email: NULL
jobName: DAVID
downloadFile: TRUE

Results:

Number of clusters: 2
Number of genes included in all clusters: 8
Number of genes included in non-filtered clusters: 8
Filtered clusters (ClusterEnrichmentScore < 0): None

Exports:
Functional network: iGraph (.RData), adjacency matrices (.RData)
Simplified cluster-terms table (shown below): simplifiedTermsTable.txt

Functional Network:

DAVID/nwFunctionalNetwork.png
Genes in several clusters:
(Different layouts)
DAVID/nwIntersection_kk.png
DAVID/nwIntersection_circle.png
Terms in several clusters:
(Marked with * in the table)
DAVID/nwTerms.png

Clusters:


Cluster 1 Score: 1.3Genes: 8 (3dw)
AlcoholismKEGG
Amine transportGO
Amphetamine addictionKEGG
Anatomical structure development *GO
Anterograde trans-synaptic signalingGO
AxonGO
Axon partGO
Axon terminusGO
BindingGO
Biological regulationGO
Biosynthetic processGO
CellGO
Cell bodyGO
Cell-cell signalingGO
Cell communicationGO
Cell partGO
Cell peripheryGO
Cell projectionGO
Cell projection partGO
Cellular localizationGO
Cellular metabolic processGO
Cellular processGO
Cellular response to stimulus *GO
Chemical synaptic transmissionGO
Cocaine addictionKEGG
CytoplasmGO
Cytoplasmic, membrane-bounded vesicleGO
Cytoplasmic partGO
Cytoplasmic vesicleGO
Developmental process *GO
Dopaminergic synapseKEGG
Endomembrane systemGO
Establishment of localizationGO
Establishment of localization in cellGO
Exocytic vesicleGO
Extracellular regionGO
Integral component of membraneGO
Integral component of plasma membraneGO
Intracellular *GO
Intracellular membrane-bounded organelleGO
Intracellular organelleGO
Intracellular partGO
Intracellular vesicleGO
Intrinsic component of membraneGO
Intrinsic component of plasma membraneGO
LocalizationGO
MembraneGO
Membrane-bounded organelleGO
Membrane-bounded vesicleGO
Membrane partGO
Metabolic processGO
Movement of cell or subcellular componentGO
Multicellular organismal processGO
Multicellular organism developmentGO
Negative regulation of biological processGO
Negative regulation of cellular processGO
Neuronal cell bodyGO
Neuron partGO
Neuron projectionGO
Neuron projection terminusGO
Neurotransmitter transportGO
Nitrogen compound transportGO
OrganelleGO
Organic substance metabolic processGO
Organic substance transportGO
Plasma membraneGO
Plasma membrane partGO
PresynapseGO
Primary metabolic processGO
Protein bindingGO
Receptor bindingGO
Regulation of biological processGO
Regulation of biological qualityGO
Regulation of cellular processGO
Regulation of localizationGO
Regulation of multicellular organismal processGO
Response to chemicalGO
Response to endogenous stimulusGO
Response to nitrogen compoundGO
Response to organic substanceGO
Response to organonitrogen compoundGO
Response to stimulusGO
Response to toxic substanceGO
Secretory vesicleGO
Serotonergic synapseKEGG
SignalingGO
Single-multicellular organism processGO
Single-organism cellular processGO
Single-organism developmental processGO
Single-organism localizationGO
Single-organism processGO
Single organism signalingGO
Single-organism transportGO
Somatodendritic compartmentGO
SynapseGO
Synapse partGO
Synaptic signalingGO
Synaptic vesicleGO
System processGO
Transmembrane transportGO
TransportGO
Transport vesicleGO
Trans-synaptic signalingGO
VesicleGO
Cluster 2 Score: 0.44Genes: 6 (2dw)
Anatomical structure development *GO
Anatomical structure morphogenesisGO
Cellular component organizationGO
Cellular component organization or biogenesisGO
Cellular response to stimulus *GO
Developmental process *GO
Intracellular *GO
Regulation of cellular component organizationGO
Regulation of developmental processGO
Signal transductionGO
* Terms marked with an asterisc are in several clusters.

Network analysis:

DAVID/nwStats.png

Potential inter-modular hubs (top betweenness in whole network):
ANKK1, KCNJ3

Potential intra-modular hubs (top betweenness within each cluster):
Cluster 1: ANKK1
Cluster 2: PDZD8
(There are no hubs in more than one cluster)

Clustering coeficient / Transitivity:
commonClustersNw1
commonGtSetsNw1

(The functional network is based on two networks/incidence matrices: common clusters and common-gene-term-sets. These are their transitivity values -probability that adjacent vertices of a vertex are connected-.)



(Page generated on Thu Jun 1 09:06:53 2017 by hwriter )