Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	CKB
	Gene name	creatine kinase, brain
	Synonyms	B-CK\|BCK\|CKBB\|HEL-211\|HEL-S-29
	Cytomap	UCSC genome browser: 14q32
	Genomic location	chr14 :103985994-103989196
	Type of gene	protein-coding
	RefGenes	NM_001823.4,
	Ensembl id	ENSG00000166165
	Description	creatine kinase B chaincreatine kinase B-typecreatine kinase-Bepididymis luminal protein 211epididymis secretory protein Li 29
	Modification date	20141222
dbXrefs	MIM : 123280
	HGNC : HGNC
	Ensembl : ENSG00000166165
	HPRD : 00423
	Vega : OTTHUMG00000171786
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CKB
	BioGPS: 1152
	Gene Expression Atlas: ENSG00000166165
	The Human Protein Atlas: ENSG00000166165
Pathway	NCI Pathway Interaction Database: CKB
	KEGG: CKB
	REACTOME: CKB
	ConsensusPathDB
	Pathway Commons: CKB
Metabolism	MetaCyc: CKB
	HUMANCyc: CKB
Regulation	Ensembl's Regulation: ENSG00000166165
	miRBase: chr14 :103,985,994-103,989,196
	TargetScan: NM_001823
	cisRED: ENSG00000166165
Context	iHOP: CKB
	cancer metabolism search in PubMed: CKB
	UCL Cancer Institute: CKB
Assigned class in ccmGDB	C

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

Cancer 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/

Metabolic Pathway Description
KEGG_ARGININE_AND_PROLINE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM
Orphanet
Disease	KEGG Disease: CKB
	MedGen: CKB (Human Medical Genetics with Condition)
	ClinVar: CKB
Phenotype	MGI: CKB (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CKB related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
EC545946	STT3A	1	66	11	125488308	125488374	CKB	59	103	14	103986331	103986376
BQ320356	CKB	16	112	14	103986637	103986893	CKB	109	221	14	103986507	103986619
AW176753	PSAP	47	85	10	73577047	73577085	CKB	85	175	14	103986228	103986318
BQ320618	CKB	29	114	14	103986637	103986879	CKB	111	223	14	103986507	103986619
CX164716	B4GALT5	1	177	20	48250835	48251011	CKB	178	574	14	103987747	103988721
BQ057560	SORBS2	1	77	4	186510307	186510383	CKB	76	532	14	103988193	103988844
AW847911	CKB	1	109	14	103988372	103988480	LSM14B	97	451	20	60701377	60704959
BP218932	CKB	2	331	14	103986496	103987652	CKB	331	407	14	103987662	103987738
BE928567	FNBP1	12	152	9	132797434	132797574	CKB	147	294	14	103988695	103988842
AI203968	CKB	135	283	14	103988182	103988402	CKB	280	526	14	103988465	103988834
AI184838	PCNP	1	102	3	101295064	101295384	CKB	99	547	14	103987665	103988699
BM690229	CKB	9	72	14	103986201	103986264	CKB	61	521	14	103986820	103988405
BQ060799	SORBS2	1	77	4	186510307	186510383	CKB	76	881	14	103986806	103988844

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr14:103988180-103988180	p.R152R	4
chr14:103986328-103986328	p.D340A	2
chr14:103986339-103986339	p.V336V	2
chr14:103986922-103986922	p.D221Y	1
chr14:103987647-103987647	p.L202L	1
chr14:103987755-103987755	p.D166E	1
chr14:103986238-103986238	p.G370D	1
chr14:103988286-103988286	p.G117D	1
chr14:103988639-103988639	p.P64P	1
chr14:103986486-103986486	p.R314W	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		2		2	1		3					2				1		2
# mutation		2		2	1		3					2				1		2
nonsynonymous SNV		1		1	1		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr14:103988481	p.A76V	1
chr14:103988639	p.P64P	1
chr14:103988688	p.P48R	1
chr14:103986328	p.T47T	1
chr14:103988690	p.R43L	1
chr14:103986486	p.D340A	1
chr14:103988703	p.R314W	1
chr14:103986510	p.E306K	1
chr14:103986541	p.V295V	1
chr14:103986585	p.L281V	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00148	creatine kinase, brain	approved; nutraceutical	Creatine

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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