SZGR2

Summary ?

GeneID	22865
Symbol	SLITRK3
Synonyms	-
Description	SLIT and NTRK like family member 3
Reference	MIM:609679\|HGNC:HGNC:23501\|Ensembl:ENSG00000121871\|HPRD:18064\|Vega:OTTHUMG00000158072
Gene type	protein-coding
Map location	3q26.1
Pascal p-value	0.669
Sherlock p-value	0.479
Fetal beta	-1.235
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
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
cg22126211	3	164914600	SLITRK3	1.42E-4	-0.358	0.031	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.

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:0007409	axonogenesis	IEA	neuron, axon, neurite (GO term level: 12)	-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
MOHANKUMAR TLX1 TARGETS DN	193	112	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
MIKKELSEN MCV6 HCP WITH H3K27ME3	435	318	All SZGR 2.0 genes in this pathway
MIKKELSEN IPS WITH HCP H3K27ME3	102	76	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
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-103/107	500	506	1A	hsa-miR-103^brain	AGCAGCAUUGUACAGGGCUAUGA
miR-103/107	500	506	1A	hsa-miR-107^brain	AGCAGCAUUGUACAGGGCUAUCA
miR-124/506	229	235	m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	229	235	m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-146	556	562	1A	hsa-miR-146a	UGAGAACUGAAUUCCAUGGGUU
miR-146	556	562	1A	hsa-miR-146b^brain	UGAGAACUGAAUUCCAUAGGCU
miR-17-5p/20/93.mr/106/519.d	942	948	m8	hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
				hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
miR-183	298	304	m8	hsa-miR-183	UAUGGCACUGGUAGAAUUCACUG
miR-217	492	498	m8	hsa-miR-217	UACUGCAUCAGGAACUGAUUGGAU
miR-30-3p	276	282	m8	hsa-miR-30a-3p	CUUUCAGUCGGAUGUUUGCAGC
miR-30-3p	276	282	m8	hsa-miR-30e-3p	CUUUCAGUCGGAUGUUUACAGC
miR-320	999	1005	m8	hsa-miR-320	AAAAGCUGGGUUGAGAGGGCGAA
miR-328	198	204	m8	hsa-miR-328^brain	CUGGCCCUCUCUGCCCUUCCGU
miR-33	490	496	m8	hsa-miR-33	GUGCAUUGUAGUUGCAUUG
miR-33	490	496	m8	hsa-miR-33b	GUGCAUUGCUGUUGCAUUGCA
miR-374	1088	1094	1A	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-381	1118	1124	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-543	254	260	1A	hsa-miR-543	AAACAUUCGCGGUGCACUUCU
miR-543	254	260	1A	hsa-miR-543	AAACAUUCGCGGUGCACUUCU
miR-93.hd/291-3p/294/295/302/372/373/520	1012	1018	m8	hsa-miR-93^brain	AAAGUGCUGUUCGUGCAGGUAG
				hsa-miR-302a	UAAGUGCUUCCAUGUUUUGGUGA
				hsa-miR-302b	UAAGUGCUUCCAUGUUUUAGUAG
				hsa-miR-302c	UAAGUGCUUCCAUGUUUCAGUGG
				hsa-miR-302d	UAAGUGCUUCCAUGUUUGAGUGU
				hsa-miR-372	AAAGUGCUGCGACAUUUGAGCGU
				hsa-miR-373	GAAGUGCUUCGAUUUUGGGGUGU
				hsa-miR-520e	AAAGUGCUUCCUUUUUGAGGG
				hsa-miR-520a	AAAGUGCUUCCCUUUGGACUGU
				hsa-miR-520b	AAAGUGCUUCCUUUUAGAGGG
				hsa-miR-520c	AAAGUGCUUCCUUUUAGAGGGUU
				hsa-miR-520d	AAAGUGCUUCUCUUUGGUGGGUU

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: SLITRK3