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Association Linkage Expression Literature GO_Annotation Gene Network miRNA Targets

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Association Linkage Expression Literature GO_Annotation Gene Network miRNA Targets Datasets Gene Ranking

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Gene Page: HDAC4

Summary

GeneID

9759

Symbol

HDAC4

Synonyms

HA6116|HD4|HDAC-A|HDACA|KIAA0288

Description

histone deacetylase 4

Locus tag

Gene type

protein-coding

Map location

2q37.3

Gene in Data Sources

Gene set name

Method of gene set

Evidence

Info

GO_Annotation

Mapping neuro-related keywords to Gene Ontology annotations

Hits with neuro-related keywords: 1

General Gene Expression (microarray) ?

Gene Expression in Brain Regions (new)

Top co-expressed genes in Brain Regions (new)

Gene

Pearson's Correlation

Spearman's Correlation

Top 10 positively co-expressed genes

AATK

0.87

0.75

TMEM184B

0.86

0.85

FAM78A

0.85

0.82

ABCA2

0.85

0.81

TNK2

0.84

0.78

NAT8L

0.84

0.80

NCKIPSD

0.83

0.79

IPO13

0.83

MAN2A2

0.83

0.76

SLC6A8

0.83

Top 10 negatively co-expressed genes

ST20

-0.45

-0.52

C9orf46

-0.44

-0.50

RP9P

-0.43

-0.56

FAM36A

-0.42

-0.41

RPL35

-0.42

-0.49

RPL24

-0.42

-0.49

RPL31

-0.41

-0.48

GTF3C6

-0.41

-0.42

SNRPG

-0.41

-0.53

RPL13AP22

-0.41

-0.62

Gene Ontology

Molecular function

GO term

Evidence

Neuro keywords

PubMed ID

GO:0003677

DNA binding

IEA

GO:0005515

protein binding

IEA

GO:0004407

histone deacetylase activity

NAS

10523670

GO:0016787

hydrolase activity

IEA

GO:0008134

transcription factor binding

TAS

12711221

GO:0016564

transcription repressor activity

IEA

GO:0016564

transcription repressor activity

TAS

10523670

Biological process

GO term

Evidence

Neuro keywords

PubMed ID

GO:0007399

nervous system development

TAS

neurite (GO term level: 5)

12711221

GO:0000122

negative regulation of transcription from RNA polymerase II promoter

IEA

GO:0001501

skeletal system development

IEA

GO:0006350

transcription

IEA

GO:0007049

cell cycle

NAS

GO:0008285

negative regulation of cell proliferation

IEA

GO:0006954

inflammatory response

TAS

12711221

GO:0007275

multicellular organismal development

NAS

GO:0016568

chromatin modification

TAS

12711221

GO:0030183

B cell differentiation

TAS

12711221

GO:0045843

negative regulation of striated muscle development

TAS

12711221

Cellular component

GO term

Evidence

Neuro keywords

PubMed ID

GO:0000118

histone deacetylase complex

TAS

12711221

GO:0005634

nucleus

NAS

GO:0005737

cytoplasm

TAS

12711221

Protein-protein Interactions

Shown by network

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ANKRD11	ANCO-1 \| LZ16 \| T13	ankyrin repeat domain 11	-	HPRD	15184363
AR	AIS \| DHTR \| HUMARA \| KD \| NR3C4 \| SBMA \| SMAX1 \| TFM	androgen receptor	Reconstituted Complex	BioGRID	12943985
BCL6	BCL5 \| BCL6A \| LAZ3 \| ZBTB27 \| ZNF51	B-cell CLL/lymphoma 6	-	HPRD,BioGRID	11929873
BCOR	ANOP2 \| FLJ20285 \| FLJ38041 \| KIAA1575 \| MAA2 \| MCOPS2 \| MGC131961 \| MGC71031	BCL6 co-repressor	-	HPRD,BioGRID	10898795
CBX5	HP1 \| HP1A	chromobox homolog 5 (HP1 alpha homolog, Drosophila)	-	HPRD,BioGRID	12242305
CTBP1	BARS \| MGC104684	C-terminal binding protein 1	Reconstituted Complex	BioGRID	11022042
EVI1	AML1-EVI-1 \| EVI-1 \| MDS1-EVI1 \| MGC163392 \| PRDM3	ecotropic viral integration site 1	-	HPRD,BioGRID	11568182
GATA1	ERYF1 \| GF-1 \| GF1 \| NFE1	GATA binding protein 1 (globin transcription factor 1)	Affinity Capture-Western Reconstituted Complex	BioGRID	14668799
HDAC3	HD3 \| RPD3 \| RPD3-2	histone deacetylase 3	-	HPRD	11804585
HDAC3	HD3 \| RPD3 \| RPD3-2	histone deacetylase 3	-	HPRD,BioGRID	11466315
HDAC4	HA6116 \| HD4 \| HDAC-A \| HDACA \| KIAA0288	histone deacetylase 4	Reconstituted Complex	BioGRID	11486037
HDAC9	DKFZp779K1053 \| HD7 \| HDAC \| HDAC7 \| HDAC7B \| HDAC9B \| HDAC9FL \| HDRP \| KIAA0744 \| MITR	histone deacetylase 9	-	HPRD,BioGRID	12590135
IKZF1	Hs.54452 \| IK1 \| IKAROS \| LYF1 \| PRO0758 \| ZNFN1A1 \| hIk-1	IKAROS family zinc finger 1 (Ikaros)	Affinity Capture-Western	BioGRID	12015313
IKZF2	HELIOS \| MGC34330 \| ZNF1A2 \| ZNFN1A2	IKAROS family zinc finger 2 (Helios)	Reconstituted Complex	BioGRID	12943985
IKZF3	AIO \| AIOLOS \| ZNFN1A3	IKAROS family zinc finger 3 (Aiolos)	Affinity Capture-Western	BioGRID	12015313
IKZF4	EOS \| KIAA1782 \| ZNFN1A4	IKAROS family zinc finger 4 (Eos)	Affinity Capture-Western	BioGRID	12015313
MAPK1	ERK \| ERK2 \| ERT1 \| MAPK2 \| P42MAPK \| PRKM1 \| PRKM2 \| p38 \| p40 \| p41 \| p41mapk	mitogen-activated protein kinase 1	-	HPRD,BioGRID	11114188
MAPK3	ERK1 \| HS44KDAP \| HUMKER1A \| MGC20180 \| P44ERK1 \| P44MAPK \| PRKM3	mitogen-activated protein kinase 3	-	HPRD,BioGRID	11114188
MEF2A	ADCAD1 \| RSRFC4 \| RSRFC9	myocyte enhancer factor 2A	-	HPRD,BioGRID	10487761
MEF2C	-	myocyte enhancer factor 2C	-	HPRD	10523670 \|11504882
MEF2C	-	myocyte enhancer factor 2C	Affinity Capture-Western Reconstituted Complex	BioGRID	10523670 \|11486037
MEF2D	DKFZp686I1536	myocyte enhancer factor 2D	-	HPRD,BioGRID	10523670
MEGF10	DKFZp781K1852 \| FLJ41574 \| KIAA1780	multiple EGF-like-domains 10	-	HPRD	12421765
NCOR1	KIAA1047 \| MGC104216 \| N-CoR \| TRAC1 \| hCIT529I10 \| hN-CoR	nuclear receptor co-repressor 1	-	HPRD	10944117 \|11804585
NCOR1	KIAA1047 \| MGC104216 \| N-CoR \| TRAC1 \| hCIT529I10 \| hN-CoR	nuclear receptor co-repressor 1	Affinity Capture-Western Reconstituted Complex	BioGRID	10640275 \|11804585
NCOR2	CTG26 \| SMRT \| SMRTE \| SMRTE-tau \| TNRC14 \| TRAC-1 \| TRAC1	nuclear receptor co-repressor 2	-	HPRD,BioGRID	11804585
NR2C1	TR2	nuclear receptor subfamily 2, group C, member 1	-	HPRD,BioGRID	11463856 \|12943985
NR2C2	TAK1 \| TR2R1 \| TR4 \| hTAK1	nuclear receptor subfamily 2, group C, member 2	Reconstituted Complex	BioGRID	12943985
PPARD	FAAR \| MGC3931 \| NR1C2 \| NUC1 \| NUCI \| NUCII \| PPAR-beta \| PPARB	peroxisome proliferator-activated receptor delta	Reconstituted Complex	BioGRID	12943985
PPARG	NR1C3 \| PPARG1 \| PPARG2 \| PPARgamma	peroxisome proliferator-activated receptor gamma	Reconstituted Complex	BioGRID	12943985
RARA	NR1B1 \| RAR	retinoic acid receptor, alpha	Reconstituted Complex	BioGRID	12943985
RBBP4	NURF55 \| RBAP48	retinoblastoma binding protein 4	Affinity Capture-Western	BioGRID	10220385
RUNX3	AML2 \| CBFA3 \| FLJ34510 \| MGC16070 \| PEBP2aC	runt-related transcription factor 3	-	HPRD	15138260
RUVBL2	CGI-46 \| ECP51 \| INO80J \| REPTIN \| RVB2 \| TIH2 \| TIP48 \| TIP49B	RuvB-like 2 (E. coli)	RUVBL2 (reptin) interacts with HDAC4.	BIND	15829968
RXRA	FLJ00280 \| FLJ00318 \| FLJ16020 \| FLJ16733 \| MGC102720 \| NR2B1	retinoid X receptor, alpha	Reconstituted Complex	BioGRID	12943985
SFN	YWHAS	stratifin	Affinity Capture-MS	BioGRID	15778465
SUMO2	HSMT3 \| MGC117191 \| SMT3B \| SMT3H2	SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae)	-	HPRD	11451954
SUV39H1	KMT1A \| MG44 \| SUV39H	suppressor of variegation 3-9 homolog 1 (Drosophila)	Affinity Capture-Western	BioGRID	12242305
TNFRSF14	ATAR \| HVEA \| HVEM \| LIGHTR \| TR2	tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)	-	HPRD	11463856
TNFSF10	APO2L \| Apo-2L \| CD253 \| TL2 \| TRAIL	tumor necrosis factor (ligand) superfamily, member 10	HDAC4 interacts with the TNFSF10 promoter.	BIND	15619633
UBE2I	C358B7.1 \| P18 \| UBC9	ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast)	Biochemical Activity	BioGRID	18691969
YWHAB	GW128 \| HS1 \| KCIP-1	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide	Affinity Capture-Western	BioGRID	10869435
YWHAE	14-3-3E \| FLJ45465 \| KCIP-1 \| MDCR \| MDS	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	Affinity Capture-Western Reconstituted Complex	BioGRID	10869435 \|11504882
YWHAE	14-3-3E \| FLJ45465 \| KCIP-1 \| MDCR \| MDS		-	HPRD	11486037
YWHAG	14-3-3GAMMA	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide	Reconstituted Complex	BioGRID	11504882
YWHAZ	KCIP-1 \| MGC111427 \| MGC126532 \| MGC138156	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	Reconstituted Complex	BioGRID	11504882
YWHAZ	KCIP-1 \| MGC111427 \| MGC126532 \| MGC138156		-	HPRD	11486037
ZBTB16	PLZF \| ZNF145	zinc finger and BTB domain containing 16	-	HPRD,BioGRID	11929873 \|15467736
ZNF354A	EZNF \| HKL1 \| KID-1 \| KID1 \| TCF17	zinc finger protein 354A	Reconstituted Complex	BioGRID	12943985

Pathway annotation

Pathway name	Pathway size	# SZGR genes in pathway	Info
BIOCARTA_CARM_ER_PATHWAY	35	27	All SZGR genes in this pathway
PID_HDAC_CLASSII_PATHWAY	34	27	All SZGR genes in this pathway
PID_HDAC_CLASSIII_PATHWAY	25	20	All SZGR genes in this pathway
PID_HDAC_CLASSI_PATHWAY	66	50	All SZGR genes in this pathway
PID_RANBP2_PATHWAY	11	11	All SZGR genes in this pathway
PID_ERA_GENOMIC_PATHWAY	65	37	All SZGR genes in this pathway
REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION	46	28	All SZGR genes in this pathway
REACTOME_SIGNALING_BY_NOTCH1	70	46	All SZGR genes in this pathway
REACTOME_SIGNALING_BY_NOTCH	103	64	All SZGR genes in this pathway
ONKEN_UVEAL_MELANOMA_UP	783	507	All SZGR genes in this pathway
ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_DN	70	38	All SZGR genes in this pathway
ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP	485	293	All SZGR genes in this pathway
CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP	39	25	All SZGR genes in this pathway
BASAKI_YBX1_TARGETS_DN	384	230	All SZGR genes in this pathway
WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN	199	124	All SZGR genes in this pathway
DACOSTA_UV_RESPONSE_VIA_ERCC3_DN	855	609	All SZGR genes in this pathway
JAZAG_TGFB1_SIGNALING_VIA_SMAD4_UP	108	66	All SZGR genes in this pathway
PUJANA_BRCA2_PCC_NETWORK	423	265	All SZGR genes in this pathway
SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN	514	330	All SZGR genes in this pathway
SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN	428	306	All SZGR genes in this pathway
KOYAMA_SEMA3B_TARGETS_DN	411	249	All SZGR genes in this pathway
PEART_HDAC_PROLIFERATION_CLUSTER_DN	76	57	All SZGR genes in this pathway
MEDINA_SMARCA4_TARGETS	44	29	All SZGR genes in this pathway
BLALOCK_ALZHEIMERS_DISEASE_UP	1691	1088	All SZGR genes in this pathway
KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN	911	527	All SZGR genes in this pathway
KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_DN	1011	592	All SZGR genes in this pathway
BONOME_OVARIAN_CANCER_SURVIVAL_SUBOPTIMAL_DEBULKING	510	309	All SZGR genes in this pathway
BERNARD_PPAPDC1B_TARGETS_DN	58	39	All SZGR genes in this pathway
BOQUEST_STEM_CELL_UP	260	174	All SZGR genes in this pathway
WEST_ADRENOCORTICAL_TUMOR_DN	546	362	All SZGR genes in this pathway
LEE_DIFFERENTIATING_T_LYMPHOCYTE	200	115	All SZGR genes in this pathway
HAN_SATB1_TARGETS_DN	442	275	All SZGR genes in this pathway
ROME_INSULIN_TARGETS_IN_MUSCLE_UP	442	263	All SZGR genes in this pathway
MARTENS_BOUND_BY_PML_RARA_FUSION	456	287	All SZGR genes in this pathway
BHAT_ESR1_TARGETS_VIA_AKT1_UP	281	183	All SZGR genes in this pathway
LEE_BMP2_TARGETS_DN	882	538	All SZGR genes in this pathway
GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP	570	339	All SZGR genes in this pathway
FORTSCHEGGER_PHF8_TARGETS_DN	784	464	All SZGR genes in this pathway
LIM_MAMMARY_STEM_CELL_UP	489	314	All SZGR genes in this pathway

miRNA Targets ?

miRNA family	Target position			miRNA ID	miRNA seq
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-1/206	3547	3553	1A	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
				hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-10	2434	2441	1A,m8	hsa-miR-10a	UACCCUGUAGAUCCGAAUUUGUG
miR-10	2434	2441	1A,m8	hsa-miR-10b	UACCCUGUAGAACCGAAUUUGU
miR-122	2929	2935	1A	hsa-miR-122a	UGGAGUGUGACAAUGGUGUUUGU
miR-124.1	734	741	1A,m8	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	734	740	1A	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
				hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
				hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
				hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-138	3280	3287	1A,m8	hsa-miR-138^brain	AGCUGGUGUUGUGAAUC
miR-140	453	459	m8	hsa-miR-140^brain	AGUGGUUUUACCCUAUGGUAG
miR-141/200a	1056	1063	1A,m8	hsa-miR-141	UAACACUGUCUGGUAAAGAUGG
miR-141/200a	1056	1063	1A,m8	hsa-miR-200a	UAACACUGUCUGGUAACGAUGU
miR-142-5p	3692	3699	1A,m8	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-155	2955	2961	m8	hsa-miR-155	UUAAUGCUAAUCGUGAUAGGGG
miR-17-5p/20/93.mr/106/519.d	3169	3176	1A,m8	hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
miR-19	3712	3718	m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	3712	3718	m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-200bc/429	1890	1896	1A	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-205	3822	3828	1A	hsa-miR-205	UCCUUCAUUCCACCGGAGUCUG
miR-22	3728	3734	m8	hsa-miR-22^brain	AAGCUGCCAGUUGAAGAACUGU
miR-29	410	416	m8	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-299-5p	451	458	1A,m8	hsa-miR-299-5p	UGGUUUACCGUCCCACAUACAU
miR-320	3730	3736	m8	hsa-miR-320	AAAAGCUGGGUUGAGAGGGCGAA
miR-365	3591	3597	m8	hsa-miR-365	UAAUGCCCCUAAAAAUCCUUAU
miR-370	3283	3289	m8	hsa-miR-370^brain	GCCUGCUGGGGUGGAACCUGG
miR-409-3p	3513	3519	m8	hsa-miR-409-3p	CGAAUGUUGCUCGGUGAACCCCU
miR-455	1477	1483	1A	hsa-miR-455	UAUGUGCCUUUGGACUACAUCG
miR-485-3p	1534	1541	1A,m8	hsa-miR-485-3p	GUCAUACACGGCUCUCCUCUCU
miR-9	2064	2070	1A	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-93.hd/291-3p/294/295/302/372/373/520	3168	3174	m8	hsa-miR-93^brain	AAAGUGCUGUUCGUGCAGGUAG
				hsa-miR-302a	UAAGUGCUUCCAUGUUUUGGUGA
				hsa-miR-302b	UAAGUGCUUCCAUGUUUUAGUAG
				hsa-miR-302c	UAAGUGCUUCCAUGUUUCAGUGG
				hsa-miR-302d	UAAGUGCUUCCAUGUUUGAGUGU
				hsa-miR-372	AAAGUGCUGCGACAUUUGAGCGU
				hsa-miR-373	GAAGUGCUUCGAUUUUGGGGUGU
				hsa-miR-520e	AAAGUGCUUCCUUUUUGAGGG
				hsa-miR-520a	AAAGUGCUUCCCUUUGGACUGU
				hsa-miR-520b	AAAGUGCUUCCUUUUAGAGGG
				hsa-miR-520c	AAAGUGCUUCCUUUUAGAGGGUU
				hsa-miR-520d	AAAGUGCUUCUCUUUGGUGGGUU

SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.