Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for CLOCK
Basic gene info.Gene symbolCLOCK
Gene nameclock circadian regulator
SynonymsKAT13D|bHLHe8
CytomapUCSC genome browser: 4q12
Genomic locationchr4 :56298659-56412997
Type of geneprotein-coding
RefGenesNM_001267843.1,
NM_004898.3,
Ensembl idENSG00000134852
Descriptioncircadian locomoter output cycles kaput proteincircadian locomoter output cycles protein kaputclass E basic helix-loop-helix protein 8clock homolog
Modification date20141222
dbXrefs MIM : 601851
HGNC : HGNC
Ensembl : ENSG00000134852
HPRD : 03508
Vega : OTTHUMG00000102141
ProteinUniProt: O15516
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CLOCK
BioGPS: 9575
Gene Expression Atlas: ENSG00000134852
The Human Protein Atlas: ENSG00000134852
PathwayNCI Pathway Interaction Database: CLOCK
KEGG: CLOCK
REACTOME: CLOCK
ConsensusPathDB
Pathway Commons: CLOCK
MetabolismMetaCyc: CLOCK
HUMANCyc: CLOCK
RegulationEnsembl's Regulation: ENSG00000134852
miRBase: chr4 :56,298,659-56,412,997
TargetScan: NM_001267843
cisRED: ENSG00000134852
ContextiHOP: CLOCK
cancer metabolism search in PubMed: CLOCK
UCL Cancer Institute: CLOCK
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for CLOCK(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CLOCK
Familial Cancer Database: CLOCK
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 601851; gene.
Orphanet
DiseaseKEGG Disease: CLOCK
MedGen: CLOCK (Human Medical Genetics with Condition)
ClinVar: CLOCK
PhenotypeMGI: CLOCK (International Mouse Phenotyping Consortium)
PhenomicDB: CLOCK

Mutations for CLOCK
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryCLOCKchr45630651056306530CLOCKchr45635227356352293
ovaryCLOCKchr45631827356318293chr87576862775768647
pancreasCLOCKchr45631126256311282CLOCKchr45631143456311454
pancreasCLOCKchr45631138656311406CLOCKchr45631615756316177
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CLOCK related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE883242CLOCK107945629957656299645CLOCK7467645629900856299610

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample 1 1    4        
GAIN (# sample) 1      4        
LOSS (# sample)   1             
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=57)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=18)
Stat. for Insertions
(# total SNVs=4)

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr4:56336954-56336954p.L123fs*117
chr4:56336953-56336954p.L123fs*143
chr4:56325088-56325088p.V255I2
chr4:56315604-56315604p.H470Y2
chr4:56315615-56315615p.H466L2
chr4:56336906-56336906p.T139N2
chr4:56348941-56348941p.T4T2
chr4:56304455-56304455p.F785L2
chr4:56304599-56304599p.A737A1
chr4:56316339-56316339p.R423G1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  75 4 21 341 113 7
# mutation1  95 4 21 341 114 9
nonsynonymous SNV1  73 3 2  341  13 8
synonymous SNV   22 1  1     1 1 1
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr4:56308750p.Q652K,CLOCK2
chr4:56304676p.G673R,CLOCK1
chr4:56345063p.T240A,CLOCK1
chr4:56315025p.S19G,CLOCK1
chr4:56325372p.R239H,CLOCK1
chr4:56308641p.D18G,CLOCK1
chr4:56345848p.S632L,CLOCK1
chr4:56315585p.S221Y,CLOCK1
chr4:56329897p.S12L,CLOCK1
chr4:56308687p.N588N,CLOCK1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for CLOCK in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for CLOCK

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

APOOL,ASXL2,BIRC6,CCNT1,CLOCK,DDI2,DNAJB14,
DPP8,EXOC6B,GTF2A1,LCOR,MAP3K2,NBEAL1,RC3H2,
REST,RIF1,RSC1A1,SON,STRN,UHMK1,WDFY3
APC,ASXL2,CLOCK,ELK4,HIPK1,HMBOX1,LMBRD2,
MAP3K2,MARCH6,MED13,NBEAL1,NHLRC2,RC3H2,RSC1A1,
STRN,TAOK1,TRIP12,TTBK2,UBR1,UHMK1,YIPF6

ANKRD17,ANKRD36BP1,ASXL2,CLOCK,DDI2,ETV3,GTF2A1,
HEATR5A,HIPK1,HIPK3,LCOR,LUZP1,MAN1A2,MAN2A1,
MYO9A,REL,REST,SON,TAOK1,TRIP11,UHMK1
CLOCK,DDI2,DHX33,DPP8,AGO2,FAM63B,HIPK3,
IL6ST,KIAA0754,LATS1,LNPEP,MAN1A2,PIK3C2A,PREX2,
PTPRG,RAD54L2,RC3H2,RIF1,SHROOM4,TAOK1,TRIM44
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for CLOCK


There's no related Drug.
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Cross referenced IDs for CLOCK
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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