SZGR2

Summary ?

GeneID	6252
Symbol	RTN1
Synonyms	NSP
Description	reticulon 1
Reference	MIM:600865\|HGNC:HGNC:10467\|Ensembl:ENSG00000139970\|HPRD:02921\|Vega:OTTHUMG00000028947
Gene type	protein-coding
Map location	14q23.1
Pascal p-value	7.069E-6
Sherlock p-value	0.957
Fetal beta	0.806
DMG	1 (# studies)
Support	G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS G2Cdb.human_clathrin G2Cdb.human_Synaptosome G2Cdb.humanNRC CompositeSet Darnell FMRP targets Potential synaptic genes

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).	2
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
cg20246273	14	60192278	RTN1	3.16E-4	0.398	0.04	DMG:Wockner_2014
cg04346701	14	60096225	RTN1	4.39E-4	0.491	0.045	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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
S100A13	0.85	0.93
FXYD1	0.84	0.92
AC021016.1	0.84	0.92
PSMB9	0.83	0.91
S100A1	0.82	0.90
BDH2	0.80	0.86
COPZ2	0.80	0.85
ROM1	0.80	0.88
TSC22D4	0.80	0.88
SERPINB6	0.80	0.88

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
LSM14B	-0.79	-0.87
PJA1	-0.79	-0.85
LASP1	-0.79	-0.86
RNASEN	-0.79	-0.86
PRCC	-0.78	-0.86
RAB35	-0.78	-0.85
PSPC1	-0.78	-0.84
FAM40A	-0.78	-0.86
HEATR5B	-0.78	-0.83
RNF40	-0.78	-0.84

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004871	signal transducer activity	NAS		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0030182	neuron differentiation	TAS	neuron (GO term level: 8)	-
GO:0007165	signal transduction	NAS		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005789	endoplasmic reticulum membrane	IEA		-
GO:0005783	endoplasmic reticulum	IEA		-
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-
GO:0030176	integral to endoplasmic reticulum membrane	TAS		8833145

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
PARENT MTOR SIGNALING UP	567	375	All SZGR 2.0 genes in this pathway
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS UP	579	346	All SZGR 2.0 genes in this pathway
DOANE RESPONSE TO ANDROGEN DN	241	146	All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 3D UP	182	110	All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 10D DN	142	90	All SZGR 2.0 genes in this pathway
SABATES COLORECTAL ADENOMA DN	291	176	All SZGR 2.0 genes in this pathway
JAATINEN HEMATOPOIETIC STEM CELL DN	226	132	All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN DN	172	112	All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS LUMINAL	326	213	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS NEUROEPITHELIUM DN	164	111	All SZGR 2.0 genes in this pathway
HASINA NOL7 TARGETS UP	13	11	All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS DN	35	22	All SZGR 2.0 genes in this pathway
LE EGR2 TARGETS DN	108	84	All SZGR 2.0 genes in this pathway
POMEROY MEDULLOBLASTOMA PROGNOSIS UP	47	30	All SZGR 2.0 genes in this pathway
GUO HEX TARGETS UP	81	54	All SZGR 2.0 genes in this pathway
LENAOUR DENDRITIC CELL MATURATION DN	128	90	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
KAYO AGING MUSCLE UP	244	165	All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY UP	487	303	All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS UP	280	183	All SZGR 2.0 genes in this pathway
LEIN NEURON MARKERS	69	45	All SZGR 2.0 genes in this pathway
WALLACE PROSTATE CANCER RACE DN	88	42	All SZGR 2.0 genes in this pathway
HANN RESISTANCE TO BCL2 INHIBITOR UP	36	24	All SZGR 2.0 genes in this pathway
TING SILENCED BY DICER	31	17	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL A UP	84	52	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN	701	446	All SZGR 2.0 genes in this pathway
ZHENG IL22 SIGNALING UP	56	36	All SZGR 2.0 genes in this pathway
LINDSTEDT DENDRITIC CELL MATURATION A	67	52	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2	491	319	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP	756	494	All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP	682	440	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP	548	370	All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM B	517	302	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-130/301	712	718	m8	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-142-5p	646	652	m8	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-19	711	717	m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	711	717	m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-26	723	729	m8	hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
miR-26	723	729	m8	hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
miR-381	526	532	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-93.hd/291-3p/294/295/302/372/373/520	714	720	1A	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: RTN1