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 CKB
Basic gene info.Gene symbolCKB
Gene namecreatine kinase, brain
SynonymsB-CK|BCK|CKBB|HEL-211|HEL-S-29
CytomapUCSC genome browser: 14q32
Genomic locationchr14 :103985994-103989196
Type of geneprotein-coding
RefGenesNM_001823.4,
Ensembl idENSG00000166165
Descriptioncreatine kinase B chaincreatine kinase B-typecreatine kinase-Bepididymis luminal protein 211epididymis secretory protein Li 29
Modification date20141222
dbXrefs MIM : 123280
HGNC : HGNC
Ensembl : ENSG00000166165
HPRD : 00423
Vega : OTTHUMG00000171786
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CKB
BioGPS: 1152
Gene Expression Atlas: ENSG00000166165
The Human Protein Atlas: ENSG00000166165
PathwayNCI Pathway Interaction Database: CKB
KEGG: CKB
REACTOME: CKB
ConsensusPathDB
Pathway Commons: CKB
MetabolismMetaCyc: CKB
HUMANCyc: CKB
RegulationEnsembl's Regulation: ENSG00000166165
miRBase: chr14 :103,985,994-103,989,196
TargetScan: NM_001823
cisRED: ENSG00000166165
ContextiHOP: CKB
cancer metabolism search in PubMed: CKB
UCL Cancer Institute: CKB
Assigned class in ccmGDBC

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Phenotypic Information for CKB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CKB
Familial Cancer Database: CKB
* 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
KEGG_ARGININE_AND_PROLINE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for CKB
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CKB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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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
There's no copy number variation information in COSMIC data for this gene.

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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=7)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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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
chr14:103988180-103988180p.R152R4
chr14:103986328-103986328p.D340A2
chr14:103986339-103986339p.V336V2
chr14:103986541-103986541p.V295V1
chr14:103988690-103988690p.T47T1
chr14:103986586-103986586p.I280I1
chr14:103988703-103988703p.R43H1
chr14:103986650-103986650p.?1
chr14:103988811-103988811p.H7P1
chr14:103986869-103986869p.I238I1

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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
# sample 2 21 3    2   1 2  
# mutation 2 21 3    2   1 2  
nonsynonymous SNV 1 11 3        1 2  
synonymous SNV 1 1       2        
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
chr14:103986585p.A76V1
chr14:103986586p.P64P1
chr14:103986629p.P48R1
chr14:103986922p.T47T1
chr14:103988481p.R43L1
chr14:103988639p.D340A1
chr14:103988688p.R314W1
chr14:103986328p.E306K1
chr14:103988690p.V295V1
chr14:103986486p.L281V1

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 CKB 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 CKB

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

ACP5,OCSTAMP,CKB,COL6A2,DAZL,DEFB124,FAM109A,
GP9,HES3,LAMC3,LCE3C,LCE3D,LGALS1,MATK,
MMP9,LINC00162,PTGDS,RCN3,RUFY4,SPRR2G,TCIRG1
AGPAT2,ALDH1L1,ASS1,AVPI1,BOK,ADIRF,C14orf180,
C20orf27,CAMK1,CKB,ECHDC3,ECHS1,FGFRL1,LGALS12,
MLXIPL,ORMDL3,PC,SHMT1,SLC25A1,TM7SF2,TMEM120A

AKAP7,CKB,DLX6,EPB41L4B,FABP1,FAM184B,FXYD3,
GPR125,HAVCR1,HMGCS2,ID3,IHH,KIAA0319,ME3,
PAQR8,PPARG,ARHGAP44,SELENBP1,SLC11A2,SLC26A2,TDP2
CKB,FXYD3,GALNT12,ILDR1,CCDC183,LSR,MAGIX,
MMP28,NHEJ1,OAF,PIGZ,PRDX6,RAB40B,RHBDL2,
RIMKLA,SLC26A6,SNX15,TMEM72,TSEN34,ZBTB22,ZBTB42
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 CKB
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00148creatine kinase, brainapproved; nutraceuticalCreatine


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Cross referenced IDs for CKB
* 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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