Gene Page: CLN3

Summary ?
GeneID1201
SymbolCLN3
SynonymsBTS|JNCL
Descriptionceroid-lipofuscinosis, neuronal 3
ReferenceMIM:607042|HGNC:HGNC:2074|Ensembl:ENSG00000188603|Ensembl:ENSG00000261832|HPRD:08450|Vega:OTTHUMG00000097024Vega:OTTHUMG00000175737
Gene typeprotein-coding
Map location16p12.1
Pascal p-value0.324
Sherlock p-value0.516
Fetal beta0.654
DMG2 (# studies)

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 2
DMG:vanEijk_2014Genome-wide DNA methylation analysisThis dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250). 2
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
GSMA_IIEGenome scan meta-analysis (European-ancestry samples)Psr: 0.01775 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 5 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg091126821628503005CLN33.43E-9-0.0092.26E-6DMG:Jaffe_2016
cg158128731628635015CLN31.928E-45.337DMG:vanEijk_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.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0048306calcium-dependent protein bindingIEA-
GO:0051082unfolded protein bindingTAS8980123 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0042133neurotransmitter metabolic processIEAneuron, axon, Synap, Neurotransmitter (GO term level: 8)-
GO:0043524negative regulation of neuron apoptosisIEAneuron (GO term level: 9)-
GO:0035235ionotropic glutamate receptor signaling pathwayIEAglutamate (GO term level: 8)-
GO:0000046autophagic vacuole fusionIEA-
GO:0001575globoside metabolic processIMP15240864 
GO:0001508regulation of action potentialIEA-
GO:0042987amyloid precursor protein catabolic processIDA10924275 
GO:0006457protein foldingTAS8980123 
GO:0016044membrane organizationIEA-
GO:0006520amino acid metabolic processIEA-
GO:0007042lysosomal lumen acidificationIMP11722572 
GO:0008306associative learningIEA-
GO:0015809arginine transportIDA16251196 
GO:0006684sphingomyelin metabolic processIMP15240864 
GO:0006681galactosylceramide metabolic processIMP15240864 
GO:0006678glucosylceramide metabolic processIMP15240864 
GO:0006898receptor-mediated endocytosisIMP15471887 
GO:0006865amino acid transportIEA-
GO:0016242negative regulation of macroautophagyIEA-
GO:0016485protein processingIEA-
GO:0050885neuromuscular process controlling balanceIEA-
GO:0030163protein catabolic processNAS10740217 
GO:0045861negative regulation of proteolysisIEA-
GO:0051453regulation of intracellular pHIDA10924275 
GO:0051480cytosolic calcium ion homeostasisIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0008021synaptic vesicleIDASynap, Neurotransmitter (GO term level: 12)10332042 |11590129 
GO:0043005neuron projectionIDAneuron, axon, neurite, dendrite (GO term level: 5)10332042 
GO:0000139Golgi membraneIDA9949212 |10191111 
GO:0005794Golgi apparatusIDA15240864 
GO:0005795Golgi stackIDA15240864 
GO:0005802trans-Golgi networkIDA15240864 
GO:0005624membrane fractionIDA12134079 
GO:0005634nucleusIDA10191116 
GO:0005737cytoplasmIDA10191116 
GO:0005739mitochondrionTAS8980123 
GO:0005765lysosomal membraneIEA-
GO:0005769early endosomeIDA15240864 
GO:0005770late endosomeIEA-
GO:0005776autophagic vacuoleIEA-
GO:0005783endoplasmic reticulumIDA10191111 
GO:0016020membraneIEA-
GO:0016021integral to membraneIDA10191112 
GO:0005901caveolaIDA15240864 
GO:0005886plasma membraneIDA10191116 |15240864 
GO:0030176integral to endoplasmic reticulum membraneIDA12706816 
GO:0044433cytoplasmic vesicle partIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG LYSOSOME 12183All SZGR 2.0 genes in this pathway
PRAMOONJAGO SOX4 TARGETS DN 5135All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL UP 450256All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 UP 380236All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 UP 418263All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 1 DN 378231All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS BASAL 330217All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747453All SZGR 2.0 genes in this pathway
BALLIF DEVELOPMENTAL DISABILITY P16 P12 DELETION 138All SZGR 2.0 genes in this pathway
WEI MYCN TARGETS WITH E BOX 795478All SZGR 2.0 genes in this pathway
RICKMAN TUMOR DIFFERENTIATED WELL VS MODERATELY UP 10969All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS 988594All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS 734436All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775494All SZGR 2.0 genes in this pathway
PENG GLUTAMINE DEPRIVATION UP 3825All SZGR 2.0 genes in this pathway
NEMETH INFLAMMATORY RESPONSE LPS UP 8864All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR UP 180125All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP 863514All SZGR 2.0 genes in this pathway
HUANG DASATINIB RESISTANCE DN 6944All SZGR 2.0 genes in this pathway
MOOTHA HUMAN MITODB 6 2002 429260All SZGR 2.0 genes in this pathway
MOOTHA MITOCHONDRIA 447277All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE 1137655All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP 745475All SZGR 2.0 genes in this pathway
KOHOUTEK CCNT1 TARGETS 5026All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D 882506All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS UP 279155All SZGR 2.0 genes in this pathway
ZWANG EGF INTERVAL DN 214124All SZGR 2.0 genes in this pathway