HCSGD entry for SMAD4

1. General information

Official gene symbol	SMAD4
Entrez ID	4089
Gene full name	SMAD family member 4
Other gene symbols	DPC4 JIP MADH4 MYHRS
Links to Entrez Gene	Links to Entrez Gene

2. Neighbors in the network

3. Gene ontology annotation

GO ID	GO term	Evidence	Category
GO:0000122	Negative regulation of transcription from RNA polymerase II promoter	TAS	biological_process
GO:0000987	Core promoter proximal region sequence-specific DNA binding	IDA	molecular_function
GO:0000988	Protein binding transcription factor activity	IDA	molecular_function
GO:0001076	RNA polymerase II transcription factor binding transcription factor activity	IEA	molecular_function
GO:0001085	RNA polymerase II transcription factor binding	IEA	molecular_function
GO:0001658	Branching involved in ureteric bud morphogenesis	IEA	biological_process
GO:0001666	Response to hypoxia	IMP	biological_process
GO:0001701	In utero embryonic development	IEA	biological_process
GO:0001702	Gastrulation with mouth forming second	IEA	biological_process
GO:0003190	Atrioventricular valve formation	IEA	biological_process
GO:0003198	Epithelial to mesenchymal transition involved in endocardial cushion formation	IEA	biological_process
GO:0003251	Positive regulation of cell proliferation involved in heart valve morphogenesis	IEA	biological_process
GO:0003279	Cardiac septum development	IEA	biological_process
GO:0003360	Brainstem development	IEA	biological_process
GO:0003677	DNA binding	IDA IEA	molecular_function
GO:0003682	Chromatin binding	IEA	molecular_function
GO:0003700	Sequence-specific DNA binding transcription factor activity	IDA IEA	molecular_function
GO:0005515	Protein binding	IPI	molecular_function
GO:0005518	Collagen binding	IEA	molecular_function
GO:0005622	Intracellular	IEA	cellular_component
GO:0005634	Nucleus	IDA IEA	cellular_component
GO:0005654	Nucleoplasm	TAS	cellular_component
GO:0005667	Transcription factor complex	IDA IEA IPI	cellular_component
GO:0005730	Nucleolus	IDA	cellular_component
GO:0005737	Cytoplasm	IDA IEA	cellular_component
GO:0005813	Centrosome	IDA	cellular_component
GO:0005829	Cytosol	TAS	cellular_component
GO:0006351	Transcription, DNA-templated	IEA TAS	biological_process
GO:0006355	Regulation of transcription, DNA-templated	IEA	biological_process
GO:0006367	Transcription initiation from RNA polymerase II promoter	TAS	biological_process
GO:0007179	Transforming growth factor beta receptor signaling pathway	IDA IEA TAS	biological_process
GO:0007183	SMAD protein complex assembly	IDA	biological_process
GO:0007411	Axon guidance	IEA	biological_process
GO:0007492	Endoderm development	IEA	biological_process
GO:0007498	Mesoderm development	IEA	biological_process
GO:0008283	Cell proliferation	IEA	biological_process
GO:0008285	Negative regulation of cell proliferation	IEA	biological_process
GO:0010467	Gene expression	TAS	biological_process
GO:0010718	Positive regulation of epithelial to mesenchymal transition	IEA ISS	biological_process
GO:0010862	Positive regulation of pathway-restricted SMAD protein phosphorylation	IEA ISS	biological_process
GO:0014033	Neural crest cell differentiation	IEA	biological_process
GO:0017015	Regulation of transforming growth factor beta receptor signaling pathway	IMP	biological_process
GO:0030308	Negative regulation of cell growth	IDA	biological_process
GO:0030509	BMP signaling pathway	IDA TAS	biological_process
GO:0030511	Positive regulation of transforming growth factor beta receptor signaling pathway	IDA	biological_process
GO:0030513	Positive regulation of BMP signaling pathway	IMP	biological_process
GO:0030616	Transforming growth factor beta receptor, common-partner cytoplasmic mediator activity	IDA	molecular_function
GO:0032444	Activin responsive factor complex	IDA	cellular_component
GO:0032525	Somite rostral/caudal axis specification	IEA	biological_process
GO:0032909	Regulation of transforming growth factor beta2 production	IMP	biological_process
GO:0035556	Intracellular signal transduction	IDA	biological_process
GO:0036302	Atrioventricular canal development	IEA	biological_process
GO:0042118	Endothelial cell activation	IEA	biological_process
GO:0042177	Negative regulation of protein catabolic process	IMP	biological_process
GO:0042802	Identical protein binding	IPI	molecular_function
GO:0042803	Protein homodimerization activity	IPI	molecular_function
GO:0043565	Sequence-specific DNA binding	IDA	molecular_function
GO:0044212	Transcription regulatory region DNA binding	IDA	molecular_function
GO:0045892	Negative regulation of transcription, DNA-templated	IDA	biological_process
GO:0045893	Positive regulation of transcription, DNA-templated	IDA	biological_process
GO:0045944	Positive regulation of transcription from RNA polymerase II promoter	IDA IEA TAS	biological_process
GO:0046872	Metal ion binding	IEA	molecular_function
GO:0048589	Developmental growth	IEA	biological_process
GO:0048663	Neuron fate commitment	IEA	biological_process
GO:0048733	Sebaceous gland development	IEA	biological_process
GO:0048859	Formation of anatomical boundary	IEA	biological_process
GO:0051098	Regulation of binding	IEA	biological_process
GO:0051797	Regulation of hair follicle development	IEA	biological_process
GO:0060021	Palate development	IEA ISS	biological_process
GO:0060391	Positive regulation of SMAD protein import into nucleus	IEA ISS	biological_process
GO:0060395	SMAD protein signal transduction	IDA	biological_process
GO:0060548	Negative regulation of cell death	IEA	biological_process
GO:0060956	Endocardial cell differentiation	IEA	biological_process
GO:0070411	I-SMAD binding	IPI	molecular_function
GO:0070412	R-SMAD binding	IPI	molecular_function
GO:0071141	SMAD protein complex	IDA	cellular_component
GO:0071559	Response to transforming growth factor beta	IDA	biological_process
GO:0072133	Metanephric mesenchyme morphogenesis	IEA	biological_process
GO:0072134	Nephrogenic mesenchyme morphogenesis	IEA	biological_process

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4. Expression levels in datasets

Meta-analysis result

p-value up	p-value down	FDR up	FDR down
0.3169090954	0.0705626952	0.9999902473	0.5015070445

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

Data source	Up or down	Log fold change
GSE11954	Down	-0.1011241085
GSE13712_SHEAR	Up	0.0984268274
GSE13712_STATIC	Down	-0.0396657292
GSE19018	Up	0.0100845781
GSE19899_A1	Down	-0.1884186577
GSE19899_A2	Down	-0.4480244327
PubMed_21979375_A1	Down	-0.5205268376
PubMed_21979375_A2	Down	-0.5224365773
GSE35957	Down	-0.2108836816
GSE36640	Down	-0.7874240924
GSE54402	Down	-0.2267686585
GSE9593	Down	-0.1175568228
GSE43922	Down	-0.5334737894
GSE24585	Up	0.0693069957
GSE37065	Up	0.2117375260
GSE28863_A1	Up	1.7470398824
GSE28863_A2	Up	1.2852726915
GSE28863_A3	Up	0.0172799526
GSE28863_A4	Down	-0.0658797191
GSE48662	Down	-0.5113316762

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-224-5p	MIMAT0000281	MIRT006527	Luciferase reporter assay//Western blot	Functional MTI	20118412
hsa-miR-26a-5p	MIMAT0000082	MIRT003803	Western blot	Functional MTI	20857419
hsa-miR-26a-5p	MIMAT0000082	MIRT003803	Luciferase reporter assay	Functional MTI	23028144
hsa-miR-483-3p	MIMAT0002173	MIRT004118	Luciferase reporter assay//qRT-PCR//Western blot	Functional MTI	21112326
hsa-miR-18a-5p	MIMAT0000072	MIRT004736	Immunoblot//Luciferase reporter assay//Microarray//qRT-PCR//Western blot	Functional MTI	20940405
hsa-miR-17-5p	MIMAT0000070	MIRT005629	Luciferase reporter assay//Microarray	Non-Functional MTI	20940405
hsa-miR-19a-3p	MIMAT0000073	MIRT005630	Luciferase reporter assay//Microarray	Non-Functional MTI	20940405
hsa-miR-20a-5p	MIMAT0000075	MIRT005631	Microarray	Non-Functional MTI (Weak)	20940405
hsa-miR-92a-3p	MIMAT0000092	MIRT005632	Microarray	Non-Functional MTI (Weak)	20940405
hsa-miR-146a-5p	MIMAT0000449	MIRT006209	Immunohistochemistry//Luciferase reporter assay//Microarray//qRT-PCR//Western blot	Functional MTI	22507670
hsa-miR-146a-5p	MIMAT0000449	MIRT006209	Luciferase reporter assay//qRT-PCR//Western blot	Functional MTI	21968601
hsa-miR-199a-5p	MIMAT0000231	MIRT007013	Luciferase reporter assay	Functional MTI	22821565
hsa-miR-199a-5p	MIMAT0000231	MIRT007013	Luciferase reporter assay	Functional MTI	22819820
hsa-miR-130a-3p	MIMAT0000425	MIRT007144	qRT-PCR	Functional MTI (Weak)	23418453
hsa-miR-130a-3p	MIMAT0000425	MIRT007144	Luciferase reporter assay	Functional MTI	23393589
hsa-miR-301a-3p	MIMAT0000688	MIRT007250	Luciferase reporter assay	Functional MTI	23393589
hsa-miR-454-3p	MIMAT0003885	MIRT007251	Luciferase reporter assay	Functional MTI	23393589
hsa-miR-182-5p	MIMAT0000259	MIRT007306	Luciferase reporter assay	Functional MTI	23226455
hsa-miR-130b-3p	MIMAT0000691	MIRT020189	Sequencing	Functional MTI (Weak)	20371350
hsa-miR-155-5p	MIMAT0000646	MIRT020774	Western blot	Non-Functional MTI	21036908
hsa-miR-186-5p	MIMAT0000456	MIRT021160	Sequencing	Functional MTI (Weak)	20371350
hsa-miR-93-5p	MIMAT0000093	MIRT028004	Sequencing	Functional MTI (Weak)	20371350
hsa-miR-19b-3p	MIMAT0000074	MIRT031156	Sequencing	Functional MTI (Weak)	20371350

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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: 1 abstracts the gene occurs.

PubMed ID of the article	Sentenece the gene occurs
23832538	Western blot and luciferase assay showed that Smad4 might be a target of miR-146a to exert miR-146a functions during photoaging
23832538	Therefore, UVA radiation-induced photoaging results in specific patterns of miRNA response and miR-146a are able to antagonize UVA-caused photoaging partially through targeting Smad4

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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 SMAD4

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: 1 abstracts the gene occurs.

PubMed ID of the article

Sentenece the gene occurs

Navigator

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