SZGR2

Summary ?

GeneID	4915
Symbol	NTRK2
Synonyms	GP145-TrkB\|TRKB\|trk-B
Description	neurotrophic tyrosine kinase, receptor, type 2
Reference	MIM:600456\|HGNC:HGNC:8032\|Ensembl:ENSG00000148053\|HPRD:02712\|Vega:OTTHUMG00000020120
Gene type	protein-coding
Map location	9q22.1
Pascal p-value	0.194
Fetal beta	-1.567
DMG	1 (# studies)
Support	TYROSINE KINASE SIGNALING G2Cdb.humanPSD G2Cdb.humanPSP CompositeSet Darnell FMRP targets

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Jaffe_2016	Genome-wide DNA methylation analysis	This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05.	1
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,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 3

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg03628748	9	87285133	NTRK2	4.08E-8	-0.022	1.15E-5	DMG:Jaffe_2016

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
ACOT8	0.94	0.90
TUSC2	0.88	0.86
MECR	0.88	0.88
UROD	0.88	0.84
MRPL17	0.87	0.88
MRPL2	0.87	0.85
SDHB	0.87	0.88
C9orf123	0.87	0.83
CDK5	0.87	0.84
COX4I1	0.87	0.86

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
EIF5B	-0.50	-0.58
AC010300.1	-0.47	-0.56
AC005921.3	-0.46	-0.65
SFRS18	-0.45	-0.59
ZNF814	-0.44	-0.53
ANKRD36B	-0.42	-0.57
ANKRD36	-0.41	-0.54
IL3RA	-0.41	-0.58
RBM25	-0.41	-0.38
AF347015.18	-0.40	-0.18

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004714	transmembrane receptor protein tyrosine kinase activity	IEA	neurite (GO term level: 8)	-
GO:0043121	neurotrophin binding	TAS	neuron (GO term level: 5)	1710174
GO:0000166	nucleotide binding	IEA		-
GO:0004872	receptor activity	IEA		-
GO:0005515	protein binding	IEA		-
GO:0005524	ATP binding	IEA		-
GO:0016740	transferase activity	IEA		-
GO:0016301	kinase activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007399	nervous system development	IEA	neurite (GO term level: 5)	-
GO:0007190	activation of adenylate cyclase activity	EXP		16805430
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	EXP		16939974
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	IEA		-
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	TAS		1710174
GO:0006468	protein amino acid phosphorylation	IEA		-
GO:0007275	multicellular organismal development	IEA		-
GO:0030154	cell differentiation	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-
GO:0005887	integral to plasma membrane	TAS		1710174

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
BDNF	MGC34632	brain-derived neurotrophic factor	-	HPRD,BioGRID	9312147
DYNLL1	DLC1 \| DLC8 \| DNCL1 \| DNCLC1 \| LC8 \| LC8a \| MGC126137 \| MGC126138 \| PIN \| hdlc1	dynein, light chain, LC8-type 1	-	HPRD,BioGRID	11157096
FRS2	FRS2A \| FRS2alpha \| SNT \| SNT-1 \| SNT1	fibroblast growth factor receptor substrate 2	Reconstituted Complex	BioGRID	10092678
FYN	MGC45350 \| SLK \| SYN	FYN oncogene related to SRC, FGR, YES	-	HPRD,BioGRID	9648856
GIPC1	C19orf3 \| GIPC \| GLUT1CBP \| Hs.6454 \| IIP-1 \| MGC15889 \| MGC3774 \| NIP \| RGS19IP1 \| SEMCAP \| SYNECTIIN \| SYNECTIN \| TIP-2	GIPC PDZ domain containing family, member 1	-	HPRD,BioGRID	11251075
KIDINS220	ARMS \| MGC163482	kinase D-interacting substrate, 220kDa	-	HPRD	15167895
NCK1	MGC12668 \| NCK \| NCKalpha	NCK adaptor protein 1	-	HPRD	12074588
NCK2	GRB4 \| NCKbeta	NCK adaptor protein 2	-	HPRD,BioGRID	12074588
NTF3	HDNF \| MGC129711 \| NGF-2 \| NGF2 \| NT3	neurotrophin 3	-	HPRD,BioGRID	8621424
NTF4	NT-4/5 \| NT4 \| NT5 \| NTF5	neurotrophin 4	Interaction between TRKB (PDB ID: 1HCF_Y) and NTF4 (PDB ID: 1HCF_A).	BIND	10388563 \|10490030 \|10631974 \|11263982 \|11738045
NTF4	NT-4/5 \| NT4 \| NT5 \| NTF5	neurotrophin 4	Interaction between TRKB (PDB ID: 1HCF_X) and NTF4 (PDB ID: 1HCF_B).	BIND	10388563 \|10490030 \|10631974 \|11263982 \|11738045
NTF4	NT-4/5 \| NT4 \| NT5 \| NTF5	neurotrophin 4	-	HPRD,BioGRID	11855816
NTF4	NT-4/5 \| NT4 \| NT5 \| NTF5	neurotrophin 4	Interaction between TRKB (PDB ID: 1HCF_Y) and NTF4 (PDB ID: 1HCF_B).	BIND	10388563 \|10490030 \|10631974 \|11263982 \|11738045
NTF4	NT-4/5 \| NT4 \| NT5 \| NTF5	neurotrophin 4	Interaction between TRKB (PDB ID: 1HCF_X) and NTF4 (PDB ID: 1HCF_A).	BIND	10388563 \|10490030 \|10631974 \|11263982 \|11738045
PIK3R1	GRB1 \| p85 \| p85-ALPHA	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	Two-hybrid	BioGRID	12074588
PLCG1	PLC-II \| PLC1 \| PLC148 \| PLCgamma1	phospholipase C, gamma 1	Reconstituted Complex Two-hybrid	BioGRID	10092678 \|12074588
PTPN1	PTP1B	protein tyrosine phosphatase, non-receptor type 1	-	HPRD,BioGRID	12237455
SH2B1	DKFZp547G1110 \| FLJ30542 \| KIAA1299 \| SH2-B \| SH2B	SH2B adaptor protein 1	Two-hybrid	BioGRID	12074588
SH2B1	DKFZp547G1110 \| FLJ30542 \| KIAA1299 \| SH2-B \| SH2B	SH2B adaptor protein 1	-	HPRD	9856458
SHC1	FLJ26504 \| SHC \| SHCA	SHC (Src homology 2 domain containing) transforming protein 1	Reconstituted Complex	BioGRID	10092678
SHC3	N-Shc \| NSHC \| RAI \| SHCC	SHC (Src homology 2 domain containing) transforming protein 3	-	HPRD,BioGRID	9507002
SQSTM1	A170 \| OSIL \| PDB3 \| ZIP3 \| p60 \| p62 \| p62B	sequestosome 1	-	HPRD,BioGRID	12471037

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG MAPK SIGNALING PATHWAY	267	205	All SZGR 2.0 genes in this pathway
KEGG NEUROTROPHIN SIGNALING PATHWAY	126	103	All SZGR 2.0 genes in this pathway
PID SHP2 PATHWAY	58	46	All SZGR 2.0 genes in this pathway
PID AJDISS 2PATHWAY	48	38	All SZGR 2.0 genes in this pathway
PID TRKR PATHWAY	62	48	All SZGR 2.0 genes in this pathway
REACTOME SIGNALLING BY NGF	217	167	All SZGR 2.0 genes in this pathway
REACTOME NGF SIGNALLING VIA TRKA FROM THE PLASMA MEMBRANE	137	105	All SZGR 2.0 genes in this pathway
TURASHVILI BREAST DUCTAL CARCINOMA VS LOBULAR NORMAL DN	69	43	All SZGR 2.0 genes in this pathway
TURASHVILI BREAST LOBULAR CARCINOMA VS DUCTAL NORMAL DN	91	53	All SZGR 2.0 genes in this pathway
TURASHVILI BREAST LOBULAR CARCINOMA VS LOBULAR NORMAL UP	94	59	All SZGR 2.0 genes in this pathway
JAEGER METASTASIS DN	258	141	All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 DN	281	186	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN	1375	806	All SZGR 2.0 genes in this pathway
HAHTOLA MYCOSIS FUNGOIDES SKIN UP	177	113	All SZGR 2.0 genes in this pathway
CHEBOTAEV GR TARGETS UP	77	62	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 1 DN	378	231	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 3 UP	329	196	All SZGR 2.0 genes in this pathway
ODONNELL METASTASIS DN	24	13	All SZGR 2.0 genes in this pathway
MATTIOLI MULTIPLE MYELOMA WITH 14Q32 TRANSLOCATIONS	36	25	All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER DN	203	134	All SZGR 2.0 genes in this pathway
SCHLESINGER METHYLATED DE NOVO IN CANCER	88	64	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 12HR DN	57	45	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN	428	306	All SZGR 2.0 genes in this pathway
RICKMAN HEAD AND NECK CANCER E	89	44	All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS	1038	678	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
BENPORATH PRC2 TARGETS	652	441	All SZGR 2.0 genes in this pathway
ASTON MAJOR DEPRESSIVE DISORDER DN	160	110	All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA MF UP	47	27	All SZGR 2.0 genes in this pathway
KANG IMMORTALIZED BY TERT DN	102	67	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR UP	240	152	All SZGR 2.0 genes in this pathway
KAAB HEART ATRIUM VS VENTRICLE UP	249	170	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR DN	504	323	All SZGR 2.0 genes in this pathway
LU AGING BRAIN UP	262	186	All SZGR 2.0 genes in this pathway
BAELDE DIABETIC NEPHROPATHY DN	434	302	All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS UP	280	183	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP	476	285	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN	701	446	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL UP	260	174	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL CULTURED VS FRESH UP	425	298	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL CULTURED VS FRESH DN	31	25	All SZGR 2.0 genes in this pathway
NAKAMURA METASTASIS	47	28	All SZGR 2.0 genes in this pathway
NAKAMURA METASTASIS MODEL UP	45	26	All SZGR 2.0 genes in this pathway
YAUCH HEDGEHOG SIGNALING PARACRINE UP	149	85	All SZGR 2.0 genes in this pathway
HUNSBERGER EXERCISE REGULATED GENES	31	26	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
DING LUNG CANCER BY MUTATION RATE	20	18	All SZGR 2.0 genes in this pathway
NAKAYAMA SOFT TISSUE TUMORS PCA1 DN	74	47	All SZGR 2.0 genes in this pathway
NAKAYAMA SOFT TISSUE TUMORS PCA2 DN	80	51	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A	898	516	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP	745	475	All SZGR 2.0 genes in this pathway
FOSTER KDM1A TARGETS UP	266	142	All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP	489	314	All SZGR 2.0 genes in this pathway
LIM MAMMARY LUMINAL MATURE DN	99	74	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-138	507	513	1A	hsa-miR-138^brain	AGCUGGUGUUGUGAAUC

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: NTRK2