TFEB (transcription factor EB)

Gene

• Entrez ID: 7942
• Gene name: Transcription factor EB
• Gene symbol: TFEB
• Synonyms (NCBI Gene): ALPHATFEB, BHLHE35, TCFEB
• Chromosome: 6
• Chromosome location: 6p21.1

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT023048	hsa-miR-124-3p	Microarray	18668037
MIRT030033	hsa-miR-26b-5p	Microarray	19088304
MIRT735164	hsa-miR-30b-5p	Luciferase reporter assay, Western blotting, Immunoprecipitaion (IP), Mass spectrometry, Immunofluorescence, qRT-PCR, In situ hybridization	32764647
MIRT1420477	hsa-miR-3184	CLIP-seq
MIRT1420478	hsa-miR-3609	CLIP-seq
MIRT1420479	hsa-miR-3616-3p	CLIP-seq
MIRT1420480	hsa-miR-423-5p	CLIP-seq
MIRT1420481	hsa-miR-4436b-3p	CLIP-seq
MIRT1420482	hsa-miR-4733-3p	CLIP-seq
MIRT1420483	hsa-miR-520g	CLIP-seq
MIRT1420484	hsa-miR-520h	CLIP-seq
MIRT1420485	hsa-miR-548ah	CLIP-seq
MIRT1420486	hsa-miR-128	CLIP-seq
MIRT1420487	hsa-miR-148a	CLIP-seq
MIRT1420488	hsa-miR-148b	CLIP-seq
MIRT1420489	hsa-miR-152	CLIP-seq
MIRT1420490	hsa-miR-3179	CLIP-seq
MIRT1420491	hsa-miR-377	CLIP-seq
MIRT1420492	hsa-miR-3944-5p	CLIP-seq
MIRT1420493	hsa-miR-4293	CLIP-seq
MIRT2126302	hsa-miR-24	CLIP-seq
MIRT1420477	hsa-miR-3184	CLIP-seq
MIRT2126303	hsa-miR-3944-3p	CLIP-seq
MIRT1420480	hsa-miR-423-5p	CLIP-seq
MIRT2126304	hsa-miR-4437	CLIP-seq
MIRT2395685	hsa-miR-1291	CLIP-seq
MIRT2395686	hsa-miR-328	CLIP-seq
MIRT2395687	hsa-miR-331-3p	CLIP-seq
MIRT2395688	hsa-miR-3689d	CLIP-seq
MIRT2395689	hsa-miR-4290	CLIP-seq
MIRT2395690	hsa-miR-4749-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000976	Function	Transcription cis-regulatory region binding	IDA	19556463
GO:0000976	Function	Transcription cis-regulatory region binding	IEA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IEA
GO:0001892	Process	Embryonic placenta development	IEA
GO:0001892	Process	Embryonic placenta development	ISS
GO:0002250	Process	Adaptive immune response	IEA
GO:0002376	Process	Immune system process	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IDA	19556463, 21617040, 22343943, 22576015, 22692423, 25720963, 32612235, 32753672, 35662396, 36749723
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0003700	Function	DNA-binding transcription factor activity	NAS	2115126
GO:0005515	Function	Protein binding	IPI	15507434, 22343943, 28514442, 28552616, 33961781, 35271311, 36931259, 37057673
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	23401004, 25720963, 32612235, 32753672, 35662396
GO:0005634	Component	Nucleus	IDA	19556463, 21617040, 22343943, 22576015, 22692423, 27278822, 28552616
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	2115126
GO:0005667	Component	Transcription regulator complex	IEA
GO:0005737	Component	Cytoplasm	IDA	19556463, 27278822
GO:0005737	Component	Cytoplasm	IEA
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IDA	22343943, 22692423, 23401004, 32612235
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005829	Component	Cytosol	IDA	21617040, 22576015, 23401004, 25720963, 32612235, 32753672, 35662396
GO:0005829	Component	Cytosol	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	NAS	2115126
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006914	Process	Autophagy	IEA
GO:0006959	Process	Humoral immune response	IEA
GO:0006959	Process	Humoral immune response	ISS
GO:0007040	Process	Lysosome organization	IDA	32612235, 32753672, 35662396
GO:0007040	Process	Lysosome organization	IEA
GO:0007040	Process	Lysosome organization	IMP	23434374
GO:0009267	Process	Cellular response to starvation	IDA	21617040
GO:0010508	Process	Positive regulation of autophagy	IDA	21617040, 22576015
GO:0010508	Process	Positive regulation of autophagy	IMP	23434374
GO:0016020	Component	Membrane	IEA
GO:0019899	Function	Enzyme binding	IPI	22576015, 22692423
GO:0032418	Process	Lysosome localization	IMP	29146937
GO:0034198	Process	Cellular response to amino acid starvation	IDA	22343943, 22576015, 22692423
GO:0045893	Process	Positive regulation of DNA-templated transcription	IDA	21617040, 22343943, 22576015, 22692423, 27278822, 29146937
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	19556463
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0046982	Function	Protein heterodimerization activity	IEA
GO:0046983	Function	Protein dimerization activity	IEA
GO:0050829	Process	Defense response to Gram-negative bacterium	IEA
GO:0140367	Process	Antibacterial innate immune response	IDA	32753672, 35662396
GO:1905671	Process	Regulation of lysosome organization	IDA	22692423, 35662396
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

Other IDs

• MIM: 600744
• HGNC: 11753
• e!Ensembl: ENSG00000112561

Protein

• UniProt ID: P19484
• Protein name: Transcription factor EB (Class E basic helix-loop-helix protein 35) (bHLHe35)
• Protein function: Transcription factor that acts as a master regulator of lysosomal biogenesis, autophagy, lysosomal exocytosis, lipid catabolism, energy metabolism and immune response (PubMed:21617040, PubMed:22343943, PubMed:22576015, PubMed:22692423, PubMed:25
• PDB: 7UX2, 7UXC, 7UXH, 7Y62
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF15951	MITF_TFEB_C_3_N	4 → 162	MITF/TFEB/TFEC/TFE3 N-terminus	Family
  PF00010	HLH	236 → 289	Helix-loop-helix DNA-binding domain	Domain
  PF11851	DUF3371	321 → 473	Domain of unknown function (DUF3371)	Family

• Sequence:

  MASRIGLRMQLMREQAQQEEQRERMQQQAVMHYMQQQQQQQQQQLGGPPTPAINTPVHFQ
  SPPPVPGEVLKVQSYLENPTSYHLQQSQHQKVREYLSETYGNKFAAHISPAQGSPKPPPA
  ASPGVRAGHVLSSSAGNSAPNSPMAMLHIGSNPERELDDVIDNIMRLDDVLGYINPEMQM
  PNTLPLSSSHLNVYSSDPQVTASLVGVTSSSCPADLTQKRELTDAESRALAKERQKKDNH
  NLIERRRRFNINDRIKELGMLIPKANDLDVRWNKGTILKASVDYIRRMQKDLQKSRELEN
  HSRRLEMTNKQLWLRIQELEMQARVHGLPTTSPSGMNMAELAQQVVKQELPSEEGPGEAL
  MLGAEVPDPEPLPALPPQAPLPLPTQPPSPFHHLDFSHSLSFGGREDEGPPGYPEPLAPG
  HGSPFPSLSKKDLDLMLLDDSLLPLASDPLLSTMSPEASKASSRRSSFSMEEGDVL

• Sequence length: 476

Pathways

KEGG:

Calcium signaling pathway
Mitophagy - animal

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LATE-ONSET ALZHEIMER'S DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Relationship Type	References	Evidence Score
Adenoma Oxyphilic	Associate	35980471	★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Associate	27813694, 28945989, 32208437	★☆☆☆☆ Found in Text Mining only
Atherosclerosis	Associate	35090378	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Associate	34663249, 35898781	★☆☆☆☆ Found in Text Mining only
Calcinosis Cutis	Associate	27565001	★☆☆☆☆ Found in Text Mining only
Carcinoma	Associate	33664427	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Associate	33960270	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Associate	18278810, 19396149, 21602817, 22446944, 22892601, 23817689, 23826432, 24618616, 26654961, 27565001, 27864122, 28338654, 28840857, 29052596, 30206412, 30383394, 30591082, 30622287, 31600176, 32217839, 32251007, 33208882, 33460450, 33664427, 33854184, 34148064, 35562857, 35971742, 35980471, 37095531, 37315151	★☆☆☆☆ Found in Text Mining only
Cardiomyopathy Dilated	Associate	36056063	★☆☆☆☆ Found in Text Mining only
Cataract	Associate	34872443	★☆☆☆☆ Found in Text Mining only
Chondrosarcoma	Associate	29035891	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Associate	26965516	★☆☆☆☆ Found in Text Mining only
Communicable Diseases	Associate	33176151	★☆☆☆☆ Found in Text Mining only
Corneal dystrophy Avellino type	Associate	32667742	★☆☆☆☆ Found in Text Mining only
Cystic Disease Of Lung	Associate	33664427	★☆☆☆☆ Found in Text Mining only
Cystinosis	Associate	26994576	★☆☆☆☆ Found in Text Mining only
Death	Associate	37936170	★☆☆☆☆ Found in Text Mining only
Dementia	Associate	32208437	★☆☆☆☆ Found in Text Mining only
Diabetic Nephropathies	Associate	33043774	★☆☆☆☆ Found in Text Mining only
Drug Related Side Effects and Adverse Reactions	Associate	35053335	★☆☆☆☆ Found in Text Mining only
Emanuel syndrome	Associate	22892601, 30622287, 32217839	★☆☆☆☆ Found in Text Mining only
Emanuel syndrome	Stimulate	27565001, 29052596, 30206412	★☆☆☆☆ Found in Text Mining only
Epidermolysis bullosa with pyloric atresia	Associate	33460450	★☆☆☆☆ Found in Text Mining only
Essential Hypertension	Associate	28682143	★☆☆☆☆ Found in Text Mining only
Familial renal cell carcinoma	Associate	34148064	★☆☆☆☆ Found in Text Mining only
Fatty Liver	Associate	34581652	★☆☆☆☆ Found in Text Mining only
Gastritis Atrophic	Associate	25551587, 30155999	★☆☆☆☆ Found in Text Mining only
Gaucher Disease	Associate	23393155, 31519738	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Associate	25482944	★☆☆☆☆ Found in Text Mining only
Glucose Intolerance	Associate	36217215	★☆☆☆☆ Found in Text Mining only
Glutamate formiminotransferase deficiency	Associate	31720741	★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease Type II	Associate	28629821	★☆☆☆☆ Found in Text Mining only
Huntington Disease	Associate	38066314	★☆☆☆☆ Found in Text Mining only
Hyperammonemia	Associate	30035657	★☆☆☆☆ Found in Text Mining only
Intervertebral Disc Degeneration	Associate	37605006	★☆☆☆☆ Found in Text Mining only
Intervertebral disc disease	Associate	37605006	★☆☆☆☆ Found in Text Mining only
Iron Overload	Associate	33410225	★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Associate	26994576, 33410225	★☆☆☆☆ Found in Text Mining only
Kidney Failure Chronic	Associate	18278810	★☆☆☆☆ Found in Text Mining only
Kidney Neoplasms	Associate	12719541, 23038766, 31600176	★☆☆☆☆ Found in Text Mining only
Leukemia	Associate	39214303	★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Associate	33860275, 39214303	★☆☆☆☆ Found in Text Mining only
Light Fixation Seizure Syndrome	Associate	27085974	★☆☆☆☆ Found in Text Mining only
Limbal Stem Cell Deficiency	Associate	27153139	★☆☆☆☆ Found in Text Mining only
Lysosomal Storage Diseases	Associate	23393155, 26994576, 33176151, 33410225, 37890378	★☆☆☆☆ Found in Text Mining only
Lysosomal Storage Diseases	Stimulate	32667742	★☆☆☆☆ Found in Text Mining only
Melanoma	Associate	30705290, 32881934, 37160873	★☆☆☆☆ Found in Text Mining only
Mitochondrial Diseases	Associate	26251447, 26509433, 36217215, 37269887	★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Associate	23221771	★☆☆☆☆ Found in Text Mining only
Muscular Disorders Atrophic	Associate	27085974	★☆☆☆☆ Found in Text Mining only
Necrosis	Associate	27565001	★☆☆☆☆ Found in Text Mining only
Neoplasm Metastasis	Associate	26654961, 29052596, 35562857	★☆☆☆☆ Found in Text Mining only
Neoplasm Metastasis	Stimulate	32753474	★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	12719541, 21602817, 23826432, 26654961, 27459917, 28547982, 29992949, 30653408, 31600176, 32251007, 33208882, 34643458, 37269887, 39196068	★☆☆☆☆ Found in Text Mining only
Neoplasms	Inhibit	24004452, 33860275, 37890378	★☆☆☆☆ Found in Text Mining only
Neoplasms	Stimulate	28837150	★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Associate	29992949, 30653408	★☆☆☆☆ Found in Text Mining only
Neurologic Manifestations	Associate	33176151	★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Associate	35053335, 37087023	★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Associate	24471499, 30086361, 39196068	★☆☆☆☆ Found in Text Mining only
Pancreatitis	Associate	36217215	★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Associate	26509433	★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Associate	27977328	★☆☆☆☆ Found in Text Mining only
Proteinuria	Inhibit	33410225	★☆☆☆☆ Found in Text Mining only
Sclerosis	Associate	27864122	★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Associate	25551587, 30155999, 32753474	★☆☆☆☆ Found in Text Mining only
Tay Sachs Disease	Associate	23393155	★☆☆☆☆ Found in Text Mining only
Tertiary Lymphoid Structures	Stimulate	35562857	★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Associate	36372230	★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Associate	37890378	★☆☆☆☆ Found in Text Mining only
X Linked Combined Immunodeficiency Diseases	Associate	31600176	★☆☆☆☆ Found in Text Mining only