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 CKM
Basic gene info.Gene symbolCKM
Gene namecreatine kinase, muscle
SynonymsCKMM|M-CK
CytomapUCSC genome browser: 19q13.32
Genomic locationchr19 :45809670-45826233
Type of geneprotein-coding
RefGenesNM_001824.4,
Ensembl idENSG00000104879
Descriptioncreatine kinase M chaincreatine kinase M-type
Modification date20141207
dbXrefs MIM : 123310
HGNC : HGNC
Ensembl : ENSG00000104879
HPRD : 00426
Vega : OTTHUMG00000181782
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CKM
BioGPS: 1158
Gene Expression Atlas: ENSG00000104879
The Human Protein Atlas: ENSG00000104879
PathwayNCI Pathway Interaction Database: CKM
KEGG: CKM
REACTOME: CKM
ConsensusPathDB
Pathway Commons: CKM
MetabolismMetaCyc: CKM
HUMANCyc: CKM
RegulationEnsembl's Regulation: ENSG00000104879
miRBase: chr19 :45,809,670-45,826,233
TargetScan: NM_001824
cisRED: ENSG00000104879
ContextiHOP: CKM
cancer metabolism search in PubMed: CKM
UCL Cancer Institute: CKM
Assigned class in ccmGDBC

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Phenotypic Information for CKM(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CKM
Familial Cancer Database: CKM
* 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: CKM
MedGen: CKM (Human Medical Genetics with Condition)
ClinVar: CKM
PhenotypeMGI: CKM (International Mouse Phenotyping Consortium)
PhenomicDB: CKM

Mutations for CKM
* 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
There's no inter-chromosomal structural variation.
- 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
pancreasCKMchr194581491045814930CACNG7chr195444632954446349
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 CKM related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF693845CKM256194582607945826133MYOZ2537334120079264120090171
F01290CKM275194581883645821136CKM72306194581504145818819
BG994088CKM8281194581502445818839PLD22743701747145174714613
DV080414MUC214141110758791078510CKM415623194581874345821178

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 # sample1                
GAIN (# sample)1                
LOSS (# sample)                 
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=31)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr19:45810883-45810883p.G268D2
chr19:45818813-45818813p.V131I2
chr19:45818835-45818835p.P123P2
chr19:45821144-45821144p.R96H2
chr19:45810756-45810756p.E310E2
chr19:45815033-45815033p.R209R2
chr19:45810133-45810133p.R341W2
chr19:45822867-45822867p.T35T1
chr19:45815077-45815077p.D195N1
chr19:45810137-45810137p.A339A1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample  181 2    21  15215
# mutation  181 2    21  15215
nonsynonymous SNV  151 2    11  12 13
synonymous SNV   3       1    32 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
chr19:45810883p.G268D2
chr19:45810118p.E346K2
chr19:45815134p.L277L1
chr19:45822867p.R96H1
chr19:45810765p.E87K1
chr19:45815158p.M272T1
chr19:45822880p.V72M1
chr19:45810845p.T35T1
chr19:45818754p.I263I1
chr19:45810857p.A31V1

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 CKM 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 CKM

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

ANKRD26P1,ATP2B3,C2orf83,CELP,CKMT2,CSTB,DMD,
FAM25BP,GALNT12,H2AFB1,H2BFM,H2BFWT,HTR5A,LCN15,
PLA2G4E,RHOXF1,RHOXF2B,SEPT14,SLC10A1,SSX4,SSX6
ABRA,ARPP21,MLIP,C8orf22,CA3,CAV3,CKMT2,
CORO6,FBXO40,HRC,LDB3,MYH1,MYOM1,NT5C1A,
PGAM2,PYGM,SLC25A4,SLC36A2,SRL,SYPL2,TNNT3

ACSF2,C8orf33,CKMT2,ERP27,EYA1,FITM2,GGH,
SLC52A2,HSF1,IFITM1,LY6G6D,MRPS28,POU5F1B,PPP1R16A,
PTP4A3,SLC30A2,SP6,SRPX2,SYN3,TNNC2,TOP1MT
ASPN,BOK,C14orf132,CAMK2A,CASQ1,CCDC136,CKMT2,
DACT3,DGKG,DMPK,DNAJB5,FREM1,HAND1,KCTD8,
MYOM1,NTM,PTRF,ARHGEF26,SLC8A1,SMYD1,SNTA1
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 CKM
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, muscleapproved; nutraceuticalCreatine
DB02490creatine kinase, muscleexperimental(Diaminomethyl-Methyl-Amino)-Acetic Acid
DB03431creatine kinase, muscleexperimentalAdenosine-5'-Diphosphate
DB04027creatine kinase, muscleexperimentalD-Arginine


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Cross referenced IDs for CKM
* 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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