SZGR2

Summary ?

GeneID	7291
Symbol	TWIST1
Synonyms	ACS3\|BPES2\|BPES3\|CRS\|CRS1\|CSO\|SCS\|TWIST\|bHLHa38
Description	twist family bHLH transcription factor 1
Reference	MIM:601622\|HGNC:HGNC:12428\|Ensembl:ENSG00000122691\|HPRD:03374\|Vega:OTTHUMG00000090821
Gene type	protein-coding
Map location	7p21.2
Pascal p-value	0.345
Fetal beta	-0.705
DMG	1 (# studies)

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:vanEijk_2014	Genome-wide DNA methylation analysis	This dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250).	1
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg24446548	7	19157263	TWIST1	0.013	2.524		DMG:vanEijk_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
UBE2D3	0.93	0.91
MOBKL3	0.93	0.93
TMED2	0.92	0.90
STRAP	0.91	0.88
RAB2A	0.91	0.89
PPP1CB	0.91	0.87
COPS3	0.90	0.85
PTGES3	0.90	0.86
OLA1	0.90	0.87
RAN	0.90	0.89

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MT-CO2	-0.71	-0.68
AF347015.26	-0.71	-0.69
AF347015.33	-0.70	-0.68
AF347015.8	-0.69	-0.68
AF347015.2	-0.69	-0.66
MT-CYB	-0.69	-0.67
AF347015.15	-0.66	-0.66
FXYD1	-0.65	-0.68
GPT	-0.65	-0.69
AF347015.31	-0.64	-0.63

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003677	DNA binding	IEA		-
GO:0005515	protein binding	IPI		18598946
GO:0004857	enzyme inhibitor activity	TAS		10025406
GO:0030528	transcription regulator activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0001764	neuron migration	IEA	neuron (GO term level: 8)	-
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	TAS		10025406
GO:0001501	skeletal system development	TAS		8988166
GO:0001843	neural tube closure	IEA		-
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0009653	anatomical structure morphogenesis	TAS		8988166
GO:0006915	apoptosis	IEA		-
GO:0007275	multicellular organismal development	IEA		-
GO:0035115	embryonic forelimb morphogenesis	IEA		-
GO:0035137	hindlimb morphogenesis	IEA		-
GO:0045843	negative regulation of striated muscle development	IEA		-
GO:0045596	negative regulation of cell differentiation	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 ARF PATHWAY	17	13	All SZGR 2.0 genes in this pathway
PID HIF2PATHWAY	34	29	All SZGR 2.0 genes in this pathway
PID HES HEY PATHWAY	48	39	All SZGR 2.0 genes in this pathway
LU TUMOR VASCULATURE UP	29	17	All SZGR 2.0 genes in this pathway
SCHUETZ BREAST CANCER DUCTAL INVASIVE UP	351	230	All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER ADVANCED VS EARLY UP	175	120	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 UP	120	73	All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN DN	172	112	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA DN	394	258	All SZGR 2.0 genes in this pathway
LI CISPLATIN RESISTANCE UP	28	20	All SZGR 2.0 genes in this pathway
WANG HCP PROSTATE CANCER	111	69	All SZGR 2.0 genes in this pathway
HOWLIN PUBERTAL MAMMARY GLAND	69	40	All SZGR 2.0 genes in this pathway
HATADA METHYLATED IN LUNG CANCER UP	390	236	All SZGR 2.0 genes in this pathway
LIAO METASTASIS	539	324	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
ONDER CDH1 TARGETS 2 UP	256	159	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
REN ALVEOLAR RHABDOMYOSARCOMA DN	408	274	All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS DN	371	218	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 8HR DN	47	31	All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1	419	273	All SZGR 2.0 genes in this pathway
GENTILE UV RESPONSE CLUSTER D8	40	29	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR DN	911	527	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR UP	783	442	All SZGR 2.0 genes in this pathway
LOPES METHYLATED IN COLON CANCER UP	27	20	All SZGR 2.0 genes in this pathway
HOQUE METHYLATED IN CANCER	56	45	All SZGR 2.0 genes in this pathway
NADELLA PRKAR1A TARGETS UP	9	5	All SZGR 2.0 genes in this pathway
WHITEFORD PEDIATRIC CANCER MARKERS	116	63	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL UP	260	174	All SZGR 2.0 genes in this pathway
LU TUMOR ENDOTHELIAL MARKERS UP	22	14	All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME2 AND H3K27ME3	59	35	All SZGR 2.0 genes in this pathway
SETLUR PROSTATE CANCER TMPRSS2 ERG FUSION UP	67	48	All SZGR 2.0 genes in this pathway
FONTAINE THYROID TUMOR UNCERTAIN MALIGNANCY DN	26	14	All SZGR 2.0 genes in this pathway
FONTAINE PAPILLARY THYROID CARCINOMA DN	80	53	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT	567	365	All SZGR 2.0 genes in this pathway
CARD MIR302A TARGETS	77	62	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-151	76	83	1A,m8	hsa-miR-151^brain	ACUAGACUGAAGCUCCUUGAGG
miR-25/32/92/363/367	676	682	1A	hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
miR-326	55	61	1A	hsa-miR-326	CCUCUGGGCCCUUCCUCCAG
miR-33	602	608	1A	hsa-miR-33	GUGCAUUGUAGUUGCAUUG
miR-33	602	608	1A	hsa-miR-33b	GUGCAUUGCUGUUGCAUUGCA
miR-361	265	271	m8	hsa-miR-361^brain	UUAUCAGAAUCUCCAGGGGUAC
miR-381	663	669	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-409-3p	568	574	m8	hsa-miR-409-3p	CGAAUGUUGCUCGGUGAACCCCU
miR-543	320	326	m8	hsa-miR-543	AAACAUUCGCGGUGCACUUCU

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: TWIST1