SZGR2

Summary ?

GeneID	50863
Symbol	NTM
Synonyms	HNT\|IGLON2\|NTRI
Description	neurotrimin
Reference	MIM:607938\|HGNC:HGNC:17941\|Ensembl:ENSG00000182667\|HPRD:06398\|Vega:OTTHUMG00000066364
Gene type	protein-coding
Map location	11q25
Pascal p-value	0.008
Fetal beta	-1.22
DMG	1 (# studies)
Support	CELL ADHESION AND TRANSSYNAPTIC SIGNALING

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWAScat	Genome-wide Association Studies	This data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGCnp	Genome-wide Association Study	GWAS
CV:Ripke_2013	Genome-wide Association Study	Multi-stage GWAS, Sweden population and PGC2. 24 leading SNPs
DMG:Montano_2016	Genome-wide DNA methylation analysis	This dataset includes 172 replicated associations between CpGs with schizophrenia.	1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg22887491	11	131618277	NTM	2.43E-5	0.005	0.067	DMG:Montano_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.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005515	protein binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0008038	neuron recognition	TAS	neuron (GO term level: 4)	7891157
GO:0007155	cell adhesion	NAS		7891157
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005886	plasma membrane	IEA		-
GO:0031225	anchored to membrane	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
WILCOX RESPONSE TO PROGESTERONE DN	66	44	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
DELYS THYROID CANCER UP	443	294	All SZGR 2.0 genes in this pathway
BEGUM TARGETS OF PAX3 FOXO1 FUSION DN	45	34	All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS DN	411	249	All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION UP	195	138	All SZGR 2.0 genes in this pathway
LEE TARGETS OF PTCH1 AND SUFU DN	83	69	All SZGR 2.0 genes in this pathway
IZADPANAH STEM CELL ADIPOSE VS BONE UP	126	92	All SZGR 2.0 genes in this pathway
YAGUE PRETUMOR DRUG RESISTANCE DN	13	11	All SZGR 2.0 genes in this pathway
MIKKELSEN IPS WITH HCP H3K27ME3	102	76	All SZGR 2.0 genes in this pathway
CHANDRAN METASTASIS UP	221	135	All SZGR 2.0 genes in this pathway
MIKKELSEN ES HCP WITH H3K27ME3	41	30	All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3	590	403	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR DN	36	19	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS DURATION CORR UP	9	7	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
WIEDERSCHAIN TARGETS OF BMI1 AND PCGF2	57	39	All SZGR 2.0 genes in this pathway
SERVITJA ISLET HNF1A TARGETS UP	163	111	All SZGR 2.0 genes in this pathway
ANASTASSIOU CANCER MESENCHYMAL TRANSITION SIGNATURE	64	40	All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY	1725	838	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	882	888	m8	hsa-miR-138^brain	AGCUGGUGUUGUGAAUC
miR-151	678	685	1A,m8	hsa-miR-151^brain	ACUAGACUGAAGCUCCUUGAGG
miR-188	629	635	m8	hsa-miR-188	CAUCCCUUGCAUGGUGGAGGGU
miR-28	1177	1183	m8	hsa-miR-28^brain	AAGGAGCUCACAGUCUAUUGAG
miR-30-5p	789	795	1A	hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
miR-346	921	927	1A	hsa-miR-346^brain	UGUCUGCCCGCAUGCCUGCCUCU
miR-361	669	675	m8	hsa-miR-361^brain	UUAUCAGAAUCUCCAGGGGUAC
miR-369-3p	1017	1023	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	1017	1023	m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-485-3p	1489	1496	1A,m8	hsa-miR-485-3p	GUCAUACACGGCUCUCCUCUCU
miR-495	1048	1054	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-495	1048	1054	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-504	1080	1086	m8	hsa-miR-504	AGACCCUGGUCUGCACUCUAU
miR-505	1129	1135	m8	hsa-miR-505	GUCAACACUUGCUGGUUUCCUC

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: NTM