SZGR2

Summary ?

GeneID	1786
Symbol	DNMT1
Synonyms	ADCADN\|AIM\|CXXC9\|DNMT\|HSN1E\|MCMT\|m.HsaI
Description	DNA (cytosine-5-)-methyltransferase 1
Reference	MIM:126375\|HGNC:HGNC:2976\|Ensembl:ENSG00000130816\|HPRD:00532\|Vega:OTTHUMG00000180397
Gene type	protein-coding
Map location	19p13.2
Pascal p-value	0.68
Sherlock p-value	0.186
TADA p-value	0.028
Fetal beta	0.778
DMG	1 (# studies)
Support	Ascano FMRP targets Chromatin Remodeling Genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Wockner_2014	Genome-wide DNA methylation analysis	This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24).	3
DNM:Gulsuner_2013	Whole Exome Sequencing analysis	155 DNMs identified by exome sequencing of quads or trios of schizophrenia individuals and their parents.
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenics,schizophrenias	Click to show details

Section I. Genetics and epigenetics annotation

DNM table

Gene	Chromosome	Position	Ref	Alt	Transcript	AA change	Mutation type	Sift	CG46	Trait	Study
DNMT1	chr19	10260563	G	T	NM_001130823 NM_001379	p.783P>T p.767P>T	missense missense			Schizophrenia	DNM:Gulsuner_2013
DNMT1	chr19	10260540	C	T	NM_001130823 NM_001379	. .	silent silent			Schizophrenia	DNM:Gulsuner_2013

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg06128182	19	10305774	DNMT1	6.09E-5	-0.216	0.023	DMG:Wockner_2014
cg01347596	19	10252900	DNMT1	1.139E-4	-0.44	0.029	DMG:Wockner_2014
cg23401624	19	10305755	DNMT1	2.349E-4	-0.381	0.037	DMG:Wockner_2014

Section II. Transcriptome annotation

General gene expression (GTEx)

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
NCSTN	0.85	0.82
VPS11	0.83	0.80
RNF26	0.82	0.83
TFG	0.82	0.78
C16orf62	0.81	0.79
C7orf42	0.81	0.83
TMEM214	0.81	0.80
PIGO	0.80	0.77
GGCX	0.79	0.77
ADIPOR1	0.79	0.74

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.21	-0.64	-0.57
MT-CO2	-0.56	-0.51
AF347015.8	-0.56	-0.50
AF347015.18	-0.56	-0.56
AF347015.31	-0.55	-0.50
AC098691.2	-0.54	-0.50
MT-ATP8	-0.53	-0.52
AF347015.2	-0.53	-0.48
AF347015.27	-0.52	-0.48
MT-CYB	-0.51	-0.46

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003677	DNA binding	IEA		-
GO:0003886	DNA (cytosine-5-)-methyltransferase activity	TAS		8940105
GO:0016740	transferase activity	IEA		-
GO:0008270	zinc ion binding	IEA		-
GO:0008134	transcription factor binding	IEA		-
GO:0008168	methyltransferase activity	IEA		-
GO:0046872	metal ion binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	TAS		10888872
GO:0006306	DNA methylation	TAS		10888872
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0006350	transcription	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	TAS		8940105

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
CBX1	CBX \| HP1-BETA \| HP1Hs-beta \| HP1Hsbeta \| M31 \| MOD1 \| p25beta	chromobox homolog 1 (HP1 beta homolog Drosophila )	-	HPRD,BioGRID	12711675
CBX5	HP1 \| HP1A	chromobox homolog 5 (HP1 alpha homolog, Drosophila)	Affinity Capture-Western	BioGRID	12867029
DMAP1	DKFZp686L09142 \| DNMAP1 \| DNMTAP1 \| EAF2 \| FLJ11543 \| KIAA1425 \| SWC4	DNA methyltransferase 1 associated protein 1	-	HPRD,BioGRID	10888872
DMAP1	DKFZp686L09142 \| DNMAP1 \| DNMTAP1 \| EAF2 \| FLJ11543 \| KIAA1425 \| SWC4	DNA methyltransferase 1 associated protein 1	DNMT1 interacts with DMAP1.	BIND	10888872
DNMT3A	DNMT3A2 \| M.HsaIIIA	DNA (cytosine-5-)-methyltransferase 3 alpha	hDNMT3a interacts with hDNMT1.	BIND	12145218
DNMT3A	DNMT3A2 \| M.HsaIIIA	DNA (cytosine-5-)-methyltransferase 3 alpha	-	HPRD,BioGRID	12145218
DNMT3B	ICF \| M.HsaIIIB	DNA (cytosine-5-)-methyltransferase 3 beta	DNMT3B interacts with DNMT1.	BIND	15120635
DNMT3B	ICF \| M.HsaIIIB	DNA (cytosine-5-)-methyltransferase 3 beta	-	HPRD,BioGRID	12145218
DNMT3B	ICF \| M.HsaIIIB	DNA (cytosine-5-)-methyltransferase 3 beta	hDNMT3b interacts with hDNMT1.	BIND	12145218
DYNLL1	DLC1 \| DLC8 \| DNCL1 \| DNCLC1 \| LC8 \| LC8a \| MGC126137 \| MGC126138 \| PIN \| hdlc1	dynein, light chain, LC8-type 1	-	HPRD	14760703
E2F1	E2F-1 \| RBAP1 \| RBBP3 \| RBP3	E2F transcription factor 1	Co-fractionation	BioGRID	10888886
HDAC1	DKFZp686H12203 \| GON-10 \| HD1 \| RPD3 \| RPD3L1	histone deacetylase 1	Co-fractionation	BioGRID	10888886
HDAC1	DKFZp686H12203 \| GON-10 \| HD1 \| RPD3 \| RPD3L1	histone deacetylase 1	-	HPRD	10615135
HDAC2	RPD3 \| YAF1	histone deacetylase 2	DNMT1 interacts with HDAC2.	BIND	10888872
HDAC2	RPD3 \| YAF1	histone deacetylase 2	-	HPRD,BioGRID	10888872
MBD2	DKFZp586O0821 \| DMTase \| NY-CO-41	methyl-CpG binding domain protein 2	-	HPRD	10947852
MBD3	-	methyl-CpG binding domain protein 3	-	HPRD	10947852
PCNA	MGC8367	proliferating cell nuclear antigen	Affinity Capture-Western Reconstituted Complex	BioGRID	9302295 \|10888872 \|12354094
PCNA	MGC8367	proliferating cell nuclear antigen	DNMT1 is a PCNA-binding protein	BIND	12171929
PCNA	MGC8367	proliferating cell nuclear antigen	-	HPRD	9302295 \|12354094
RARB	HAP \| NR1B2 \| RRB2	retinoic acid receptor, beta	DNMT1 interacts with RARB (RAR-beta-2) gene promoter sequences.	BIND	15688037
RB1	OSRC \| RB \| p105-Rb \| pRb \| pp110	retinoblastoma 1	Rb interacts with hDnmt1.	BIND	11847125
RB1	OSRC \| RB \| p105-Rb \| pRb \| pp110	retinoblastoma 1	-	HPRD,BioGRID	10888886
RGS6	DKFZp313G1241 \| FLJ43552 \| GAP \| MGC142132	regulator of G-protein signaling 6	Reconstituted Complex	BioGRID	14734556
SUV39H1	KMT1A \| MG44 \| SUV39H	suppressor of variegation 3-9 homolog 1 (Drosophila)	-	HPRD,BioGRID	12711675
TRIM27	RFP \| RNF76	tripartite motif-containing 27	Two-hybrid	BioGRID	16169070
TSG101	TSG10 \| VPS23	tumor susceptibility gene 101	-	HPRD	10888872

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG CYSTEINE AND METHIONINE METABOLISM	34	24	All SZGR 2.0 genes in this pathway
PID RB 1PATHWAY	65	46	All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR UP	557	331	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP	1278	748	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED UP	633	376	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP	722	443	All SZGR 2.0 genes in this pathway
KOKKINAKIS METHIONINE DEPRIVATION 48HR DN	64	39	All SZGR 2.0 genes in this pathway
KOKKINAKIS METHIONINE DEPRIVATION 96HR DN	75	50	All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE DN	485	334	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS UP	126	72	All SZGR 2.0 genes in this pathway
MARKEY RB1 CHRONIC LOF UP	115	78	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION UP	552	347	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA UP	536	340	All SZGR 2.0 genes in this pathway
MISSIAGLIA REGULATED BY METHYLATION DN	122	67	All SZGR 2.0 genes in this pathway
OZANNE AP1 TARGETS UP	18	11	All SZGR 2.0 genes in this pathway
RIZ ERYTHROID DIFFERENTIATION	77	51	All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS UP	414	287	All SZGR 2.0 genes in this pathway
DAIRKEE TERT TARGETS UP	380	213	All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER UP	358	245	All SZGR 2.0 genes in this pathway
PUJANA XPRSS INT NETWORK	168	103	All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK	1652	1023	All SZGR 2.0 genes in this pathway
PUJANA BRCA2 PCC NETWORK	423	265	All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK	1442	892	All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK	779	480	All SZGR 2.0 genes in this pathway
PUJANA BRCA CENTERED NETWORK	117	72	All SZGR 2.0 genes in this pathway
WEI MYCN TARGETS WITH E BOX	795	478	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN	514	330	All SZGR 2.0 genes in this pathway
MORI IMMATURE B LYMPHOCYTE DN	90	55	All SZGR 2.0 genes in this pathway
SHEPARD BMYB MORPHOLINO DN	200	112	All SZGR 2.0 genes in this pathway
PENG RAPAMYCIN RESPONSE UP	203	130	All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA UP	64	46	All SZGR 2.0 genes in this pathway
YAMAZAKI TCEB3 TARGETS DN	215	132	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 3	101	64	All SZGR 2.0 genes in this pathway
RAMPON ENRICHED LEARNING ENVIRONMENT EARLY UP	15	12	All SZGR 2.0 genes in this pathway
JACKSON DNMT1 TARGETS DN	25	21	All SZGR 2.0 genes in this pathway
SIMBULAN PARP1 TARGETS DN	17	10	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS PEAK AT 16HR	40	24	All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP	566	371	All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED	728	415	All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS	212	121	All SZGR 2.0 genes in this pathway
GAZIN EPIGENETIC SILENCING BY KRAS	26	16	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP	973	570	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP	863	514	All SZGR 2.0 genes in this pathway
WHITEFORD PEDIATRIC CANCER MARKERS	116	63	All SZGR 2.0 genes in this pathway
LABBE WNT3A TARGETS UP	112	71	All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR UP	294	199	All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB DN	342	220	All SZGR 2.0 genes in this pathway
LINDSTEDT DENDRITIC CELL MATURATION D	68	44	All SZGR 2.0 genes in this pathway
HOFFMANN LARGE TO SMALL PRE BII LYMPHOCYTE UP	163	102	All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR DN	277	166	All SZGR 2.0 genes in this pathway
CHEN METABOLIC SYNDROM NETWORK	1210	725	All SZGR 2.0 genes in this pathway
ZHAN V1 LATE DIFFERENTIATION GENES DN	15	13	All SZGR 2.0 genes in this pathway
PUJANA BREAST CANCER WITH BRCA1 MUTATED UP	56	27	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP	605	377	All SZGR 2.0 genes in this pathway
WONG EMBRYONIC STEM CELL CORE	335	193	All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR UP	324	193	All SZGR 2.0 genes in this pathway
CARD MIR302A TARGETS	77	62	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN	1972	1213	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN	882	538	All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS DN	553	343	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP	570	339	All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family	Target position			miRNA ID	miRNA seq
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-148/152	48	55	1A,m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU

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.

Gene Page: DNMT1