Gene Page:CLN3

Summary?
GeneID 1201
Symbol CLN3
Synonyms BTS|JNCL
Description ceroid-lipofuscinosis, neuronal 3
Reference MIM:607042|HGNC:HGNC:2074|Ensembl:ENSG00000188603|Ensembl:ENSG00000261832|HPRD:08450|Vega:OTTHUMG00000097024Vega:OTTHUMG00000175737
Gene type protein-coding
Map location 16p12.1
Pascal p-value 0.324
Sherlock p-value 0.516
Fetal beta 0.654
DMG 2 (# studies)

Gene in Data Sources
Gene set name Method of gene set Description Info
DMG:Jaffe_2016 Genome-wide DNA methylation analysis This 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_2014 Genome-wide DNA methylation analysis This dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250). 2
PMID:cooccur High-throughput literature-search 系统搜索PubMed co-o基因ccurring with SCZ keywords. A total of 3027 genes were included.
GSMA_IIE Genome scan meta-analysis (European-ancestry samples) Psr: 0.01775
Literature High-throughput literature-search Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias Click to show details
GO_Annotation Mapping neuro-related keywords to Gene Ontology annotations Hits with neuro-related keywords: 5

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg09112682 16 28503005 CLN3 3.43E-9 -0.009 2.26E-6 DMG:Jaffe_2016
cg15812873 16 28635015 CLN3 1.928E-4 5.337 DMG: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 function 去的术语 Evidence Neuro keywords PubMed ID
GO:0048306 calcium-dependent protein binding IEA -
GO:0051082 unfolded protein binding TAS 8980123
Biological process 去的术语 Evidence Neuro keywords PubMed ID
GO:0042133 neurotransmitter metabolic process IEA neuron, axon, Synap, Neurotransmitter (GO term level: 8) -
GO:0043524 negative regulation of neuron apoptosis IEA neuron (GO term level: 9) -
GO:0035235 ionotropic glutamate receptor signaling pathway IEA glutamate (GO term level: 8) -
GO:0000046 autophagic vacuole fusion IEA -
GO:0001575 globoside metabolic process IMP 15240864
GO:0001508 regulation of action potential IEA -
GO:0042987 amyloid precursor protein catabolic process IDA 10924275
GO:0006457 protein folding TAS 8980123
GO:0016044 membrane organization IEA -
GO:0006520 amino acid metabolic process IEA -
GO:0007042 lysosomal lumen acidification IMP 11722572
GO:0008306 associative learning IEA -
GO:0015809 arginine transport IDA 16251196
GO:0006684 sphingomyelin metabolic process IMP 15240864
GO:0006681 galactosylceramide metabolic process IMP 15240864
GO:0006678 glucosylceramide metabolic process IMP 15240864
GO:0006898 receptor-mediated endocytosis IMP 15471887
GO:0006865 amino acid transport IEA -
GO:0016242 negative regulation of macroautophagy IEA -
GO:0016485 protein processing IEA -
GO:0050885 neuromuscular process controlling balance IEA -
GO:0030163 protein catabolic process NAS 10740217
GO:0045861 negative regulation of proteolysis IEA -
去:0051453 regulation of intracellular pH IDA 10924275
GO:0051480 cytosolic calcium ion homeostasis IEA -
Cellular component 去的术语 Evidence Neuro keywords PubMed ID
GO:0008021 synaptic vesicle IDA Synap, Neurotransmitter (GO term level: 12) 10332042|11590129
GO:0043005 neuron projection IDA neuron, axon, neurite, dendrite (GO term level: 5) 10332042
GO:0000139 Golgi membrane IDA 9949212|10191111
GO:0005794 Golgi apparatus IDA 15240864
GO:0005795 Golgi stack IDA 15240864
GO:0005802 trans-Golgi network IDA 15240864
GO:0005624 membrane fraction IDA 12134079
GO:0005634 nucleus IDA 10191116
GO:0005737 cytoplasm IDA 10191116
GO:0005739 mitochondrion TAS 8980123
GO:0005765 lysosomal membrane IEA -
GO:0005769 early endosome IDA 15240864
GO:0005770 late endosome IEA -
GO:0005776 autophagic vacuole IEA -
GO:0005783 endoplasmic reticulum IDA 10191111
GO:0016020 membrane IEA -
GO:0016021 integral to membrane IDA 10191112
GO:0005901 caveola IDA 15240864
GO:0005886 plasma membrane IDA 10191116|15240864
GO:0030176 integral to endoplasmic reticulum membrane IDA 12706816
GO:0044433 cytoplasmic vesicle part IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG LYSOSOME 121 83 All SZGR 2.0 genes in this pathway
PRAMOONJAGO SOX4 TARGETS DN 51 35 All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL UP 450 256 All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 UP 380 236 All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 UP 418 263 All SZGR 2.0 genes in this pathway
林格伦膀胱癌集群1 DN 378 231 All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS BASAL 330 217 All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747 453 All SZGR 2.0 genes in this pathway
BALLIF DEVELOPMENTAL DISABILITY P16 P12 DELETION 13 8 All SZGR 2.0 genes in this pathway
WEI MYCN TARGETS WITH E BOX 795 478 All SZGR 2.0 genes in this pathway
RICKMAN TUMOR DIFFERENTIATED WELL VS MODERATELY UP 109 69 All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS 988 594 All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS 734 436 All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775 494 All SZGR 2.0 genes in this pathway
PENG GLUTAMINE DEPRIVATION UP 38 25 All SZGR 2.0 genes in this pathway
NEMETH INFLAMMATORY RESPONSE LPS UP 88 64 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR UP 180 125 All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP 863 514 All SZGR 2.0 genes in this pathway
HUANG DASATINIB RESISTANCE DN 69 44 All SZGR 2.0 genes in this pathway
MOOTHA HUMAN MITODB 6 2002 429 260 All SZGR 2.0 genes in this pathway
MOOTHA MITOCHONDRIA 447 277 All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103 714 All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 1972 1213 All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE 1137 655 All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP 745 475 All SZGR 2.0 genes in this pathway
KOHOUTEK CCNT1 TARGETS 50 26 All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D 882 506 All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS UP 279 155 All SZGR 2.0 genes in this pathway
ZWANG EGF INTERVAL DN 214 124 All SZGR 2.0 genes in this pathway