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:

Genes in several clusters:

(Different layouts)

Terms in several clusters:

(Marked with * in the table)

Clusters:

Cluster 1

Score: 1.3

Genes: (3dw)

Alcoholism	KEGG
Amine transport	GO
Amphetamine addiction	KEGG
Anatomical structure development *	GO
Anterograde trans-synaptic signaling	GO
Axon	GO
Axon part	GO
Axon terminus	GO
Binding	GO
Biological regulation	GO
Biosynthetic process	GO
Cell	GO
Cell body	GO
Cell-cell signaling	GO
Cell communication	GO
Cell part	GO
Cell periphery	GO
Cell projection	GO
Cell projection part	GO
Cellular localization	GO
Cellular metabolic process	GO
Cellular process	GO
Cellular response to stimulus *	GO
Chemical synaptic transmission	GO
Cocaine addiction	KEGG
Cytoplasm	GO
Cytoplasmic, membrane-bounded vesicle	GO
Cytoplasmic part	GO
Cytoplasmic vesicle	GO
Developmental process *	GO
Dopaminergic synapse	KEGG
Endomembrane system	GO
Establishment of localization	GO
Establishment of localization in cell	GO
Exocytic vesicle	GO
Extracellular region	GO
Integral component of membrane	GO
Integral component of plasma membrane	GO
Intracellular *	GO
Intracellular membrane-bounded organelle	GO
Intracellular organelle	GO
Intracellular part	GO
Intracellular vesicle	GO
Intrinsic component of membrane	GO
Intrinsic component of plasma membrane	GO
Localization	GO
Membrane	GO
Membrane-bounded organelle	GO
Membrane-bounded vesicle	GO
Membrane part	GO
Metabolic process	GO
Movement of cell or subcellular component	GO
Multicellular organismal process	GO
Multicellular organism development	GO
Negative regulation of biological process	GO
Negative regulation of cellular process	GO
Neuronal cell body	GO
Neuron part	GO
Neuron projection	GO
Neuron projection terminus	GO
Neurotransmitter transport	GO
Nitrogen compound transport	GO
Organelle	GO
Organic substance metabolic process	GO
Organic substance transport	GO
Plasma membrane	GO
Plasma membrane part	GO
Presynapse	GO
Primary metabolic process	GO
Protein binding	GO
Receptor binding	GO
Regulation of biological process	GO
Regulation of biological quality	GO
Regulation of cellular process	GO
Regulation of localization	GO
Regulation of multicellular organismal process	GO
Response to chemical	GO
Response to endogenous stimulus	GO
Response to nitrogen compound	GO
Response to organic substance	GO
Response to organonitrogen compound	GO
Response to stimulus	GO
Response to toxic substance	GO
Secretory vesicle	GO
Serotonergic synapse	KEGG
Signaling	GO
Single-multicellular organism process	GO
Single-organism cellular process	GO
Single-organism developmental process	GO
Single-organism localization	GO
Single-organism process	GO
Single organism signaling	GO
Single-organism transport	GO
Somatodendritic compartment	GO
Synapse	GO
Synapse part	GO
Synaptic signaling	GO
Synaptic vesicle	GO
System process	GO
Transmembrane transport	GO
Transport	GO
Transport vesicle	GO
Trans-synaptic signaling	GO
Vesicle	GO

Cluster 2

Score: 0.44

Genes: (2dw)

Anatomical structure development *	GO
Anatomical structure morphogenesis	GO
Cellular component organization	GO
Cellular component organization or biogenesis	GO
Cellular response to stimulus *	GO
Developmental process *	GO
Intracellular *	GO
Regulation of cellular component organization	GO
Regulation of developmental process	GO
Signal transduction	GO

* Terms marked with an asterisc are in several clusters.

Network analysis:

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:

commonClustersNw	1
commonGtSetsNw	1

(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 )