SZGR2

Summary ?

GeneID	9421
Symbol	HAND1
Synonyms	Hxt\|Thing1\|bHLHa27\|eHand
Description	heart and neural crest derivatives expressed 1
Reference	MIM:602406\|HGNC:HGNC:4807\|Ensembl:ENSG00000113196\|HPRD:03871\|Vega:OTTHUMG00000130193
Gene type	protein-coding
Map location	5q33
Pascal p-value	0.015
Fetal beta	-0.384
DMG	1 (# studies)

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).	1
GSMA_I	Genome scan meta-analysis	Psr: 0.0032
GSMA_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.01718
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.00459

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg25587535	5	153857846	HAND1	2.288E-4	-0.255	0.036	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
MAVS	0.89	0.88
NUP210	0.87	0.87
EIF2C1	0.87	0.82
SP1	0.87	0.84
MAML1	0.86	0.83
ZNF516	0.86	0.87
PDPR	0.85	0.84
FAM53B	0.84	0.86
CTDSP2	0.84	0.85
KIAA0355	0.84	0.84

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.31	-0.48	-0.55
AF347015.21	-0.47	-0.64
C5orf53	-0.47	-0.50
RERGL	-0.47	-0.61
IFI27	-0.46	-0.50
GMFG	-0.46	-0.60
C1orf54	-0.46	-0.60
SYCP3	-0.46	-0.58
CARD16	-0.45	-0.56
MYL3	-0.45	-0.53

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003700	transcription factor activity	TAS		9931445
GO:0008134	transcription factor binding	IEA		-
GO:0016564	transcription repressor activity	IEA		-
GO:0042803	protein homodimerization activity	IEA		-
GO:0046982	protein heterodimerization activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	IEA		-
GO:0001525	angiogenesis	IEA		-
GO:0001707	mesoderm formation	IEA		-
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0007507	heart development	TAS		9931445
GO:0007275	multicellular organismal development	IEA		-
GO:0030154	cell differentiation	IEA		-
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
BIOCARTA NFAT PATHWAY	56	45	All SZGR 2.0 genes in this pathway
MAHADEVAN IMATINIB RESISTANCE DN	20	11	All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA PROGRESSION RISK	74	44	All SZGR 2.0 genes in this pathway
RIZ ERYTHROID DIFFERENTIATION 12HR	43	35	All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS	1174	695	All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM5	94	59	All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS	1062	725	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL AND BRAIN QTL TRANS	185	114	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
NOUZOVA METHYLATED IN APL	68	39	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL LONG TERM	302	191	All SZGR 2.0 genes in this pathway
XU GH1 EXOGENOUS TARGETS UP	85	50	All SZGR 2.0 genes in this pathway
XU GH1 AUTOCRINE TARGETS UP	268	157	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3 UNMETHYLATED	536	296	All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K27ME3	269	159	All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3	590	403	All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP	857	456	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
let-7/98	744	751	1A,m8	hsa-let-7a^brain	UGAGGUAGUAGGUUGUAUAGUU
				hsa-let-7b^brain	UGAGGUAGUAGGUUGUGUGGUU
				hsa-let-7c^brain	UGAGGUAGUAGGUUGUAUGGUU
				hsa-let-7d^brain	AGAGGUAGUAGGUUGCAUAGU
				hsa-let-7e^brain	UGAGGUAGGAGGUUGUAUAGU
				hsa-let-7f^brain	UGAGGUAGUAGAUUGUAUAGUU
				hsa-miR-98^brain	UGAGGUAGUAAGUUGUAUUGUU
				hsa-let-7g^SZ	UGAGGUAGUAGUUUGUACAGU
				hsa-let-7i^brain	UGAGGUAGUAGUUUGUGCUGU
miR-196	684	691	1A,m8	hsa-miR-196a	UAGGUAGUUUCAUGUUGUUGG
miR-196	684	691	1A,m8	hsa-miR-196b	UAGGUAGUUUCCUGUUGUUGG
miR-25/32/92/363/367	175	181	m8	hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
				hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
miR-33	431	437	1A	hsa-miR-33	GUGCAUUGUAGUUGCAUUG
miR-33	431	437	1A	hsa-miR-33b	GUGCAUUGCUGUUGCAUUGCA
miR-335	803	810	1A,m8	hsa-miR-335^brain	UCAAGAGCAAUAACGAAAAAUGU
miR-363	174	180	m8	hsa-miR-363	AUUGCACGGUAUCCAUCUGUAA

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: HAND1