Gene Page: CLOCK

Summary ?
GeneID9575
SymbolCLOCK
SynonymsKAT13D|bHLHe8
Descriptionclock circadian regulator
ReferenceMIM:601851|HGNC:HGNC:2082|Ensembl:ENSG00000134852|HPRD:03508|Vega:OTTHUMG00000102141
Gene typeprotein-coding
Map location4q12
Pascal p-value0.05
Sherlock p-value0.792
Fetal beta-0.55
DMG1 (# studies)
eGeneCerebellum

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). 1
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
AssociationA combined odds ratio method (Sun et al. 2008), association studies1Link to SZGene
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenics,schizophreniasClick to show details

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg25530661456301576CLOCK2.402E-4-0.3160.037DMG: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
PRRT30.860.91
NDRG40.860.87
RPS6KA40.850.87
PINK10.850.88
COPS7A0.850.87
PPAPDC30.840.87
ANXA60.840.81
GRIN10.840.86
PLD30.840.86
AP001107.10.830.87
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
RBMX2-0.50-0.53
C9orf46-0.47-0.50
EXOSC8-0.46-0.43
GTF3C6-0.46-0.47
C21orf57-0.45-0.46
DYNLT1-0.44-0.51
RPS25P8-0.44-0.53
RPS8-0.44-0.46
RPS20-0.44-0.54
ZNF300-0.44-0.17

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0004871signal transducer activityIEA-
GO:0003700transcription factor activityIEA-
GO:0003700transcription factor activityTAS10198158 
GO:0005515protein bindingIEA-
GO:0004402histone acetyltransferase activityIEA-
GO:0016740transferase activityIEA-
GO:0008415acyltransferase activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0007165signal transductionIEA-
GO:0007165signal transductionTAS10198158 
GO:0009648photoperiodismTAS10198158 
GO:0007623circadian rhythmIEA-
GO:0007623circadian rhythmTAS10198158 
GO:0045944positive regulation of transcription from RNA polymerase II promoterIEA-
GO:0045944positive regulation of transcription from RNA polymerase II promoterIGI9576906 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIEA-
GO:0005667transcription factor complexIEA-
GO:0005667transcription factor complexIPI9576906 
GO:0005730nucleolusIDA18029348 
GO:0005737cytoplasmIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG CIRCADIAN RHYTHM MAMMAL 1313All SZGR 2.0 genes in this pathway
PID CIRCADIAN PATHWAY 1615All SZGR 2.0 genes in this pathway
REACTOME BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION 3627All SZGR 2.0 genes in this pathway
REACTOME PPARA ACTIVATES GENE EXPRESSION 10472All SZGR 2.0 genes in this pathway
REACTOME RORA ACTIVATES CIRCADIAN EXPRESSION 2417All SZGR 2.0 genes in this pathway
REACTOME CIRCADIAN REPRESSION OF EXPRESSION BY REV ERBA 2316All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS 478302All SZGR 2.0 genes in this pathway
REACTOME FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 168115All SZGR 2.0 genes in this pathway
REACTOME CIRCADIAN CLOCK 5340All SZGR 2.0 genes in this pathway
RODRIGUES NTN1 TARGETS DN 158102All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN 17811082All SZGR 2.0 genes in this pathway
STREICHER LSM1 TARGETS UP 4434All SZGR 2.0 genes in this pathway
RIZ ERYTHROID DIFFERENTIATION 7751All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN 855609All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 COMMON DN 483336All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER UP 358245All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM4 261153All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN DN 584395All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN 848527All SZGR 2.0 genes in this pathway
MORI SMALL PRE BII LYMPHOCYTE UP 8657All SZGR 2.0 genes in this pathway
PENG RAPAMYCIN RESPONSE UP 203130All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR UP 240152All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN 830547All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 5 12678All SZGR 2.0 genes in this pathway
STEARMAN LUNG CANCER EARLY VS LATE UP 12589All SZGR 2.0 genes in this pathway
TAYLOR METHYLATED IN ACUTE LYMPHOBLASTIC LEUKEMIA 7752All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A4 196124All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS UP 518299All SZGR 2.0 genes in this pathway
GABRIELY MIR21 TARGETS 289187All SZGR 2.0 genes in this pathway
CARD MIR302A TARGETS 7762All SZGR 2.0 genes in this pathway
IVANOVSKA MIR106B TARGETS 9056All SZGR 2.0 genes in this pathway
IKEDA MIR30 TARGETS UP 11687All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-1/206230623121Ahsa-miR-1UGGAAUGUAAAGAAGUAUGUA
hsa-miR-206SZUGGAAUGUAAGGAAGUGUGUGG
hsa-miR-613AGGAAUGUUCCUUCUUUGCC
miR-124/50612051211m8hsa-miR-506UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brainUAAGGCACGCGGUGAAUGCC
miR-130/301912918m8hsa-miR-130abrainCAGUGCAAUGUUAAAAGGGCAU
hsa-miR-301CAGUGCAAUAGUAUUGUCAAAGC
hsa-miR-130bbrainCAGUGCAAUGAUGAAAGGGCAU
hsa-miR-454-3pUAGUGCAAUAUUGCUUAUAGGGUUU
miR-148/152913919m8hsa-miR-148aUCAGUGCACUACAGAACUUUGU
hsa-miR-152brainUCAGUGCAUGACAGAACUUGGG
hsa-miR-148bUCAGUGCAUCACAGAACUUUGU
miR-15/16/195/424/497797803m8hsa-miR-15abrainUAGCAGCACAUAAUGGUUUGUG
hsa-miR-16brainUAGCAGCACGUAAAUAUUGGCG
hsa-miR-15bbrainUAGCAGCACAUCAUGGUUUACA
hsa-miR-195SZUAGCAGCACAGAAAUAUUGGC
hsa-miR-424CAGCAGCAAUUCAUGUUUUGAA
hsa-miR-497CAGCAGCACACUGUGGUUUGU
miR-17-5p/20/93.mr/106/519.d10691075m8hsa-miR-17-5pCAAAGUGCUUACAGUGCAGGUAGU
hsa-miR-20abrainUAAAGUGCUUAUAGUGCAGGUAG
hsa-miR-106aAAAAGUGCUUACAGUGCAGGUAGC
hsa-miR-106bSZUAAAGUGCUGACAGUGCAGAU
hsa-miR-20bSZCAAAGUGCUCAUAGUGCAGGUAG
hsa-miR-519dCAAAGUGCCUCCCUUUAGAGUGU
miR-1822712781A,m8hsa-miR-182UUUGGCAAUGGUAGAACUCACA
miR-19104810551A,m8hsa-miR-19aUGUGCAAAUCUAUGCAAAACUGA
hsa-miR-19bUGUGCAAAUCCAUGCAAAACUGA
miR-190211821251A,m8hsa-miR-190UGAUAUGUUUGAUAUAUUAGGU
miR-30-5p6977041A,m8hsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA
miR-409-3p10781084m8hsa-miR-409-3pCGAAUGUUGCUCGGUGAACCCCU
miR-495775781m8hsa-miR-495brainAAACAAACAUGGUGCACUUCUUU
miR-542-3p7687741Ahsa-miR-542-3pUGUGACAGAUUGAUAACUGAAA
miR-54310231029m8hsa-miR-543AAACAUUCGCGGUGCACUUCU
hsa-miR-543AAACAUUCGCGGUGCACUUCU
miR-9205420611A,m8hsa-miR-9SZUCUUUGGUUAUCUAGCUGUAUGA
miR-962722781Ahsa-miR-96brainUUUGGCACUAGCACAUUUUUGC