SZGR2

Summary ?

GeneID	9392
Symbol	TGFBRAP1
Synonyms	TRAP-1\|TRAP1\|VPS3
Description	transforming growth factor beta receptor associated protein 1
Reference	MIM:606237\|HGNC:HGNC:16836\|Ensembl:ENSG00000135966\|HPRD:06948\|Vega:OTTHUMG00000130809
Gene type	protein-coding
Map location	2q12.1
Pascal p-value	0.027
Fetal beta	-0.091
DMG	1 (# studies)
eGene	Myers' cis & trans

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: 0.0004
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.00755

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg14459716	2	105889560	TGFBRAP1	3.926E-4	0.458	0.043	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs7595584	chr2	175652187	TGFBRAP1	9392	0.04	trans
rs17029291	chr3	32402138	TGFBRAP1	9392	0.02	trans
rs830202	chr3	165654796	TGFBRAP1	9392	0.01	trans
rs17160578	chr7	85672108	TGFBRAP1	9392	0.09	trans
rs722970	chr7	85803264	TGFBRAP1	9392	0.04	trans
rs17324099	chr7	85856288	TGFBRAP1	9392	0.08	trans
rs12569493	chr10	74886042	TGFBRAP1	9392	0.1	trans
rs16930362	chr10	74890320	TGFBRAP1	9392	0.04	trans
rs7092445	chr10	74921991	TGFBRAP1	9392	0.13	trans
rs16915029	chr10	75001994	TGFBRAP1	9392	0.1	trans
rs12571454	chr10	75208954	TGFBRAP1	9392	0.15	trans
rs16958358	chr17	55502410	TGFBRAP1	9392	0.02	trans
rs1761450	chr19	54818034	TGFBRAP1	9392	0.04	trans
rs6032295	chr20	44178138	TGFBRAP1	9392	0.15	trans
rs6098023	chr20	53113740	TGFBRAP1	9392	0.13	trans
rs17264923	chrX	69499164	TGFBRAP1	9392	0.05	trans

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
NOP56	0.88	0.88
DDX56	0.87	0.85
TRAPPC3	0.87	0.85
WIBG	0.87	0.87
EXOSC7	0.86	0.86
PSMD13	0.86	0.87
NGDN	0.86	0.88
KAT5	0.86	0.87
C1orf174	0.86	0.85
BCS1L	0.85	0.87

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MT-CO2	-0.78	-0.74
AF347015.8	-0.77	-0.76
MT-CYB	-0.77	-0.76
AF347015.2	-0.77	-0.77
AF347015.31	-0.76	-0.75
AF347015.27	-0.76	-0.77
AF347015.15	-0.75	-0.76
AF347015.26	-0.75	-0.77
AF347015.33	-0.75	-0.74
AF347015.9	-0.70	-0.73

Section III. Gene Ontology annotation

Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005737	cytoplasm	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ACVR1B	ACTRIB \| ACVRLK4 \| ALK4 \| SKR2	activin A receptor, type IB	-	HPRD	11278302
ACVR2B	ACTRIIB \| ActR-IIB \| MGC116908	activin A receptor, type IIB	-	HPRD	11278302
ACVRL1	ACVRLK1 \| ALK-1 \| ALK1 \| HHT \| HHT2 \| ORW2 \| SKR3 \| TSR-I	activin A receptor type II-like 1	-	HPRD	11278302
ALOX5	5-LO \| 5-LOX \| 5LPG \| LOG5 \| MGC163204	arachidonate 5-lipoxygenase	-	HPRD,BioGRID	10051563
ALOX5	5-LO \| 5-LOX \| 5LPG \| LOG5 \| MGC163204	arachidonate 5-lipoxygenase	5LO interacts with TRAP-1.	BIND	10051563
BMPR1A	10q23del \| ACVRLK3 \| ALK3 \| CD292	bone morphogenetic protein receptor, type IA	-	HPRD	11278302
SMAD2	JV18 \| JV18-1 \| MADH2 \| MADR2 \| MGC22139 \| MGC34440 \| hMAD-2 \| hSMAD2	SMAD family member 2	-	HPRD	11278302
SMAD4	DPC4 \| JIP \| MADH4	SMAD family member 4	-	HPRD,BioGRID	11278302
TGFB1	CED \| DPD1 \| TGFB \| TGFbeta	transforming growth factor, beta 1	Affinity Capture-Western	BioGRID	11278302
TGFB2	MGC116892 \| TGF-beta2	transforming growth factor, beta 2	Affinity Capture-Western	BioGRID	11278302
TGFBR1	AAT5 \| ACVRLK4 \| ALK-5 \| ALK5 \| LDS1A \| LDS2A \| SKR4 \| TGFR-1	transforming growth factor, beta receptor 1	-	HPRD	11278302
TGFBR2	AAT3 \| FAA3 \| LDS1B \| LDS2B \| MFS2 \| RIIC \| TAAD2 \| TGFR-2 \| TGFbeta-RII	transforming growth factor, beta receptor II (70/80kDa)	-	HPRD	11278302

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
PID SMAD2 3PATHWAY	17	13	All SZGR 2.0 genes in this pathway
PID TGFBR PATHWAY	55	38	All SZGR 2.0 genes in this pathway
WANG CLIM2 TARGETS UP	269	146	All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 DN	242	165	All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 DN	281	186	All SZGR 2.0 genes in this pathway
JAATINEN HEMATOPOIETIC STEM CELL UP	316	190	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 3 UP	329	196	All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS	1174	695	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR UP	240	152	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 12HR UP	111	68	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 DN	1011	592	All SZGR 2.0 genes in this pathway
BREDEMEYER RAG SIGNALING VIA ATM NOT VIA NFKB DN	38	23	All SZGR 2.0 genes in this pathway
CHANDRAN METASTASIS UP	221	135	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN	1972	1213	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE EARLY LATE	317	190	All SZGR 2.0 genes in this pathway

Gene Page: TGFBRAP1