HCSGD entry for TRAF6

1. General information

Official gene symbol	TRAF6
Entrez ID	7189
Gene full name	TNF receptor-associated factor 6, E3 ubiquitin protein ligase
Other gene symbols	MGC:3310 RNF85
Links to Entrez Gene	Links to Entrez Gene

2. Neighbors in the network

This gene isn't in PPI subnetwork.

3. Gene ontology annotation

GO ID	GO term	Evidence	Category
GO:0000122	Negative regulation of transcription from RNA polymerase II promoter	IMP	biological_process
GO:0000187	Activation of MAPK activity	TAS	biological_process
GO:0000209	Protein polyubiquitination	IDA	biological_process
GO:0001503	Ossification	IEA	biological_process
GO:0001843	Neural tube closure	IEA	biological_process
GO:0002224	Toll-like receptor signaling pathway	TAS	biological_process
GO:0002726	Positive regulation of T cell cytokine production	IMP	biological_process
GO:0002755	MyD88-dependent toll-like receptor signaling pathway	TAS	biological_process
GO:0002756	MyD88-independent toll-like receptor signaling pathway	TAS	biological_process
GO:0004842	Ubiquitin-protein ligase activity	EXP IDA TAS	molecular_function
GO:0004871	Signal transducer activity	IEA	molecular_function
GO:0005515	Protein binding	IPI	molecular_function
GO:0005634	Nucleus	IDA	cellular_component
GO:0005730	Nucleolus	IDA	cellular_component
GO:0005737	Cytoplasm	IDA	cellular_component
GO:0005811	Lipid particle	ISS	cellular_component
GO:0005829	Cytosol	TAS	cellular_component
GO:0005886	Plasma membrane	IDA TAS	cellular_component
GO:0005938	Cell cortex	IEA	cellular_component
GO:0006461	Protein complex assembly	IEA	biological_process
GO:0007249	I-kappaB kinase/NF-kappaB signaling	TAS	biological_process
GO:0007250	Activation of NF-kappaB-inducing kinase activity	IMP	biological_process
GO:0007254	JNK cascade	TAS	biological_process
GO:0008270	Zinc ion binding	IEA	molecular_function
GO:0009898	Cytoplasmic side of plasma membrane	ISS	cellular_component
GO:0010008	Endosome membrane	TAS	cellular_component
GO:0019886	Antigen processing and presentation of exogenous peptide antigen via MHC class II	IEA	biological_process
GO:0019901	Protein kinase binding	IPI	molecular_function
GO:0030316	Osteoclast differentiation	IEA	biological_process
GO:0031293	Membrane protein intracellular domain proteolysis	TAS	biological_process
GO:0031398	Positive regulation of protein ubiquitination	NAS	biological_process
GO:0031435	Mitogen-activated protein kinase kinase kinase binding	IPI	molecular_function
GO:0031625	Ubiquitin protein ligase binding	IPI	molecular_function
GO:0031666	Positive regulation of lipopolysaccharide-mediated signaling pathway	IEA	biological_process
GO:0031965	Nuclear membrane	IDA	cellular_component
GO:0031996	Thioesterase binding	IPI	molecular_function
GO:0032147	Activation of protein kinase activity	IDA	biological_process
GO:0032743	Positive regulation of interleukin-2 production	IMP	biological_process
GO:0034134	Toll-like receptor 2 signaling pathway	TAS	biological_process
GO:0034138	Toll-like receptor 3 signaling pathway	TAS	biological_process
GO:0034142	Toll-like receptor 4 signaling pathway	TAS	biological_process
GO:0034146	Toll-like receptor 5 signaling pathway	TAS	biological_process
GO:0034162	Toll-like receptor 9 signaling pathway	TAS	biological_process
GO:0034166	Toll-like receptor 10 signaling pathway	TAS	biological_process
GO:0035631	CD40 receptor complex	ISS	cellular_component
GO:0035666	TRIF-dependent toll-like receptor signaling pathway	TAS	biological_process
GO:0035872	Nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway	TAS	biological_process
GO:0038095	Fc-epsilon receptor signaling pathway	TAS	biological_process
GO:0038123	Toll-like receptor TLR1:TLR2 signaling pathway	TAS	biological_process
GO:0038124	Toll-like receptor TLR6:TLR2 signaling pathway	TAS	biological_process
GO:0042088	T-helper 1 type immune response	IEA	biological_process
GO:0042102	Positive regulation of T cell proliferation	IEA	biological_process
GO:0042475	Odontogenesis of dentin-containing tooth	IEA	biological_process
GO:0042826	Histone deacetylase binding	IPI	molecular_function
GO:0043011	Myeloid dendritic cell differentiation	IEA	biological_process
GO:0043065	Positive regulation of apoptotic process	TAS	biological_process
GO:0043066	Negative regulation of apoptotic process	TAS	biological_process
GO:0043123	Positive regulation of I-kappaB kinase/NF-kappaB signaling	IDA TAS	biological_process
GO:0043422	Protein kinase B binding	IPI	molecular_function
GO:0043507	Positive regulation of JUN kinase activity	IDA NAS	biological_process
GO:0045084	Positive regulation of interleukin-12 biosynthetic process	IEA	biological_process
GO:0045087	Innate immune response	TAS	biological_process
GO:0045410	Positive regulation of interleukin-6 biosynthetic process	IEA	biological_process
GO:0045453	Bone resorption	IEA	biological_process
GO:0045672	Positive regulation of osteoclast differentiation	IDA	biological_process
GO:0045892	Negative regulation of transcription, DNA-templated	IMP	biological_process
GO:0045944	Positive regulation of transcription from RNA polymerase II promoter	IDA NAS	biological_process
GO:0047485	Protein N-terminus binding	IPI	molecular_function
GO:0048011	Neurotrophin TRK receptor signaling pathway	TAS	biological_process
GO:0048468	Cell development	IEA	biological_process
GO:0048471	Perinuclear region of cytoplasm	IDA	cellular_component
GO:0048661	Positive regulation of smooth muscle cell proliferation	IEA	biological_process
GO:0050852	T cell receptor signaling pathway	IMP TAS	biological_process
GO:0050870	Positive regulation of T cell activation	IC	biological_process
GO:0051023	Regulation of immunoglobulin secretion	IEA	biological_process
GO:0051091	Positive regulation of sequence-specific DNA binding transcription factor activity	IMP	biological_process
GO:0051092	Positive regulation of NF-kappaB transcription factor activity	IDA IMP TAS	biological_process
GO:0051403	Stress-activated MAPK cascade	TAS	biological_process
GO:0051865	Protein autoubiquitination	IDA TAS	biological_process
GO:0070423	Nucleotide-binding oligomerization domain containing signaling pathway	TAS	biological_process
GO:0070498	Interleukin-1-mediated signaling pathway	IEA	biological_process
GO:0070534	Protein K63-linked ubiquitination	IDA IGI	biological_process
GO:0070555	Response to interleukin-1	IDA	biological_process
GO:0097190	Apoptotic signaling pathway	TAS	biological_process
GO:2000679	Positive regulation of transcription regulatory region DNA binding	IDA	biological_process

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4. Expression levels in datasets

Meta-analysis result

p-value up	p-value down	FDR up	FDR down
0.2193213594	0.8103027051	0.9007267124	1.0000000000

Individual experiment result
( "-" represent NA in the specific microarray platform )

Data source	Up or down	Log fold change
GSE11954	Up	0.0300423904
GSE13712_SHEAR	Up	0.0906658426
GSE13712_STATIC	Up	0.1879630342
GSE19018	Down	-0.0653962614
GSE19899_A1	Down	-0.0260984328
GSE19899_A2	Up	0.2971916544
PubMed_21979375_A1	Down	-0.1396166689
PubMed_21979375_A2	Up	0.8186427236
GSE35957	Up	0.1512429332
GSE36640	Up	0.4505225060
GSE54402	Up	0.1904052114
GSE9593	Up	0.2293796083
GSE43922	Up	0.0622279931
GSE24585	Down	-0.1217021246
GSE37065	Up	0.3315457529
GSE28863_A1	Up	0.0643823905
GSE28863_A2	Up	0.2023463255
GSE28863_A3	Down	-0.2441200934
GSE28863_A4	Down	-0.1858270455
GSE48662	Down	-0.4554130870

5. Regulation relationships with compounds/drugs/microRNAs

Compounds

Not regulated by compounds

Drugs

Not regulated by drugs

MicroRNAs

mirTarBase

MiRNA_name	mirBase ID	miRTarBase ID	Experiment	Support type	References (Pubmed ID)
hsa-miR-146a-5p	MIMAT0000449	MIRT000711	Western blot//Northern blot	Functional MTI	18504431
hsa-miR-146a-5p	MIMAT0000449	MIRT000711	Luciferase reporter assay//Western blot	Functional MTI	20061417
hsa-miR-146a-5p	MIMAT0000449	MIRT000711	qRT-PCR//flow//Luciferase reporter assay//Western blot	Functional MTI	20375304
hsa-miR-146a-5p	MIMAT0000449	MIRT000711	qRT-PCR	Functional MTI (Weak)	18759964
hsa-miR-146a-5p	MIMAT0000449	MIRT000711	Immunoprecipitaion//Western blot//Communoprecipitaion	Functional MTI	19898489
hsa-miR-146a-5p	MIMAT0000449	MIRT000711	qRT-PCR//Western blot//Immunofluorescence	Functional MTI	19918258
hsa-miR-146a-5p	MIMAT0000449	MIRT000711	Luciferase reporter assay//Microarray//Northern blot//qRT-PCR	Functional MTI	16885212
hsa-miR-146a-5p	MIMAT0000449	MIRT000711	ELISA//Luciferase reporter assay//Northern blot//qRT-PCR//Western blot	Functional MTI	20542134
hsa-miR-146a-5p	MIMAT0000449	MIRT000711	qRT-PCR//Western blot	Functional MTI	21178010
hsa-miR-146a-5p	MIMAT0000449	MIRT000711	Luciferase reporter assay	Functional MTI	22593544
hsa-miR-146a-5p	MIMAT0000449	MIRT000711	Western blot	Functional MTI	20110513
hsa-miR-146b-5p	MIMAT0002809	MIRT005394	Luciferase reporter assay//Microarray//Northern blot//qRT-PCR	Functional MTI	16885212

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mirRecord

No target information from mirRecord

6. Text-mining results about the gene

Gene occurances in abstracts of cellular senescence-associated articles: 2 abstracts the gene occurs.

PubMed ID of the article	Sentenece the gene occurs
24337384	We identified a conserved TNFR-associated factor 6 (TRAF6) binding motif, which was required for CD158d-induced NF-kappaB activation and IL-8 secretion, TRAF6 association with CD158d, and TRAF6 recruitment to CD158d(+) endosomes in transfected cells
23252865	We also observed that the expressions of IRAK1 and TRAF6, the targets of miR-146a, and DC-SIGN, a target of miR-155 were diminished while miR-146a and miR-155 were augmented during aging
23252865	In addition, we found that the production of pro-inflammatory cytokines, which is mediated by the activation of NF-kB pathway via IRAK1 and TRAF6, was greatly reduced in aged BMDC

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Navigator

1.General information
2.Neighbors in the network
3.Gene Ontology Annotation
4.Expression levels
5.Regulation
6.Text-mining results

HCSGD entry for TRAF6

1. General information

2. Neighbors in the network

3. Gene ontology annotation

GO ID

GO term

Evidence

Category

4. Expression levels in datasets

Meta-analysis result

Individual experiment result ( "-" represent NA in the specific microarray platform )

( "-" represent NA in the specific microarray platform )

5. Regulation relationships with compounds/drugs/microRNAs

Compounds

Drugs

MicroRNAs

mirTarBase

MiRNA_name

mirBase ID

miRTarBase ID

Experiment

Support type

References (Pubmed ID)

mirRecord

6. Text-mining results about the gene

Gene occurances in abstracts of cellular senescence-associated articles: 2 abstracts the gene occurs.

PubMed ID of the article

Sentenece the gene occurs

Navigator

Individual experiment result
( "-" represent NA in the specific microarray platform )