Summary ?
GeneID6252
SymbolRTN1
SynonymsNSP
Descriptionreticulon 1
ReferenceMIM:600865|HGNC:HGNC:10467|Ensembl:ENSG00000139970|HPRD:02921|Vega:OTTHUMG00000028947
Gene typeprotein-coding
Map location14q23.1
Pascal p-value7.069E-6
Sherlock p-value0.957
Fetal beta0.806
DMG1 (# studies)
SupportG2Cdb.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 setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 2
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg202462731460192278RTN13.16E-40.3980.04DMG:Wockner_2014
cg043467011460096225RTN14.39E-40.4910.045DMG:Wockner_2014


Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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
GenePearson's Correlation Spearman's Correlation
S100A130.850.93
FXYD10.840.92
AC021016.10.840.92
PSMB90.830.91
S100A10.820.90
BDH20.800.86
COPZ20.800.85
ROM10.800.88
TSC22D40.800.88
SERPINB60.800.88
Top 10 negatively co-expressed genes
GenePearson'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 functionGO termEvidenceNeuro keywordsPubMed ID
GO:0004871signal transducer activityNAS-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0030182neuron differentiationTASneuron (GO term level: 8)-
GO:0007165signal transductionNAS-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005789endoplasmic reticulum membraneIEA-
GO:0005783endoplasmic reticulumIEA-
GO:0016020membraneIEA-
GO:0016021integral to membraneIEA-
GO:0030176integral to endoplasmic reticulum membraneTAS8833145 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PARENT MTOR SIGNALING UP 567375All SZGR 2.0 genes in this pathway
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS UP 579346All SZGR 2.0 genes in this pathway
DOANE RESPONSE TO ANDROGEN DN 241146All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 3D UP 182110All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 10D DN 14290All SZGR 2.0 genes in this pathway
SABATES COLORECTAL ADENOMA DN 291176All SZGR 2.0 genes in this pathway
JAATINEN HEMATOPOIETIC STEM CELL DN 226132All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN DN 172112All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS LUMINAL 326213All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS NEUROEPITHELIUM DN 164111All SZGR 2.0 genes in this pathway
HASINA NOL7 TARGETS UP 1311All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS DN 3522All SZGR 2.0 genes in this pathway
LE EGR2 TARGETS DN 10884All SZGR 2.0 genes in this pathway
POMEROY MEDULLOBLASTOMA PROGNOSIS UP 4730All SZGR 2.0 genes in this pathway
GUO HEX TARGETS UP 8154All SZGR 2.0 genes in this pathway
LENAOUR DENDRITIC CELL MATURATION DN 12890All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
KAYO AGING MUSCLE UP 244165All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY UP 487303All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS UP 280183All SZGR 2.0 genes in this pathway
LEIN NEURON MARKERS 6945All SZGR 2.0 genes in this pathway
WALLACE PROSTATE CANCER RACE DN 8842All SZGR 2.0 genes in this pathway
HANN RESISTANCE TO BCL2 INHIBITOR UP 3624All SZGR 2.0 genes in this pathway
TING SILENCED BY DICER 3117All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL A UP 8452All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN 701446All SZGR 2.0 genes in this pathway
ZHENG IL22 SIGNALING UP 5636All SZGR 2.0 genes in this pathway
LINDSTEDT DENDRITIC CELL MATURATION A 6752All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305895All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 491319All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP 756494All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP 682440All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP 548370All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM B 517302All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-130/301712718m8hsa-miR-130abrainCAGUGCAAUGUUAAAAGGGCAU
hsa-miR-301CAGUGCAAUAGUAUUGUCAAAGC
hsa-miR-130bbrainCAGUGCAAUGAUGAAAGGGCAU
hsa-miR-454-3pUAGUGCAAUAUUGCUUAUAGGGUUU
miR-142-5p646652m8hsa-miR-142-5pCAUAAAGUAGAAAGCACUAC
miR-19711717m8hsa-miR-19aUGUGCAAAUCUAUGCAAAACUGA
hsa-miR-19bUGUGCAAAUCCAUGCAAAACUGA
miR-26723729m8hsa-miR-26abrainUUCAAGUAAUCCAGGAUAGGC
hsa-miR-26bSZUUCAAGUAAUUCAGGAUAGGUU
miR-3815265321Ahsa-miR-381UAUACAAGGGCAAGCUCUCUGU
miR-93.hd/291-3p/294/295/302/372/373/5207147201Ahsa-miR-93brainAAAGUGCUGUUCGUGCAGGUAG
hsa-miR-302aUAAGUGCUUCCAUGUUUUGGUGA
hsa-miR-302bUAAGUGCUUCCAUGUUUUAGUAG
hsa-miR-302cUAAGUGCUUCCAUGUUUCAGUGG
hsa-miR-302dUAAGUGCUUCCAUGUUUGAGUGU
hsa-miR-372AAAGUGCUGCGACAUUUGAGCGU
hsa-miR-373GAAGUGCUUCGAUUUUGGGGUGU
hsa-miR-520eAAAGUGCUUCCUUUUUGAGGG
hsa-miR-520aAAAGUGCUUCCCUUUGGACUGU
hsa-miR-520bAAAGUGCUUCCUUUUAGAGGG
hsa-miR-520cAAAGUGCUUCCUUUUAGAGGGUU
hsa-miR-520dAAAGUGCUUCUCUUUGGUGGGUU