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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 CACNB2

Basic gene info.	Gene symbol	CACNB2
	Gene name	calcium channel, voltage-dependent, beta 2 subunit
	Synonyms	CACNLB2\|CAVB2\|MYSB
	Cytomap	UCSC genome browser: 10p12
	Genomic location	chr10 :18429605-18830688
	Type of gene	protein-coding
	RefGenes	NM_000724.3, NM_001167945.1,NM_201570.2,NM_201571.3,NM_201572.3, NM_201590.2,NM_201593.2,NM_201596.2,NM_201597.2,
	Ensembl id	ENSG00000165995
	Description	CAB2calcium channel voltage-dependent subunit beta 2lambert-Eaton myasthenic syndrome antigen Bmyasthenic (Lambert-Eaton) syndrome antigen Bvoltage-dependent L-type calcium channel subunit beta-2
	Modification date	20141219
dbXrefs	MIM : 600003
	HGNC : HGNC
	Ensembl : ENSG00000165995
	HPRD : 02473
	Vega : OTTHUMG00000017764
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CACNB2
	BioGPS: 783
	Gene Expression Atlas: ENSG00000165995
	The Human Protein Atlas: ENSG00000165995
Pathway	NCI Pathway Interaction Database: CACNB2
	KEGG: CACNB2
	REACTOME: CACNB2
	ConsensusPathDB
	Pathway Commons: CACNB2
Metabolism	MetaCyc: CACNB2
	HUMANCyc: CACNB2
Regulation	Ensembl's Regulation: ENSG00000165995
	miRBase: chr10 :18,429,605-18,830,688
	TargetScan: NM_000724
	cisRED: ENSG00000165995
Context	iHOP: CACNB2
	cancer metabolism search in PubMed: CACNB2
	UCL Cancer Institute: CACNB2
Assigned class in ccmGDB	C

Top

Phenotypic Information for CACNB2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CACNB2
	Familial Cancer Database: CACNB2

* 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
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: CACNB2
	MedGen: CACNB2 (Human Medical Genetics with Condition)
	ClinVar: CACNB2
Phenotype	MGI: CACNB2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CACNB2

Mutations for CACNB2

* 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

- Statistics for Tissue and Mutation type

Top

- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	CACNB2	chr10	18765925	18765945		chr10	32438586	32438606
ovary	CACNB2	chr10	18786368	18786388	CACNB2	chr10	18787524	18787544
pancreas	CACNB2	chr10	18771559	18771579	CACNB2	chr10	18772786	18772806
prostate	CACNB2	chr10	18775843	18775843		chr10	111523505	111523505

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CACNB2 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
DA505169	MAP9	1	202	4	156297921	156298122	CACNB2	199	515	10	18802449	18834460
CB962120	CACNB2	1	413	10	18499947	18500360	SPARCL1	402	612	4	88401541	88403655
BF222031	KLK3	1	172	19	51363849	51364020	CACNB2	171	248	10	18484079	18484156
BQ380638	PTPRK	25	46	6	128407537	128407558	CACNB2	45	70	10	18679996	18680030
BF921318	CACNB2	21	321	10	18827246	18828413	NUP98	313	553	11	3793058	3797143
BF922976	CACNB2	5	320	10	18827246	18828431	NUP98	312	586	11	3793058	3797177
AW005394	CACNB2	5	183	10	18820778	18822031	PCGF2	181	638	17	36894605	36895928

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

Top

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

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=72)	Stat. for Synonymous SNVs (# total SNVs=16)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=1)

Top

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
chr10:18828550-18828550	p.R572H	4
chr10:18828421-18828421	p.S529L	3
chr10:18828493-18828493	p.R553H	3
chr10:18828510-18828510	p.R559R	3
chr10:18823074-18823074	p.A320V	2
chr10:18789772-18789772	p.L108S	2
chr10:18828645-18828645	p.R604C	2
chr10:18690935-18690935	p.A44G	2
chr10:18690937-18690937	p.E45K	2
chr10:18827148-18827148	p.D393N	2

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2	3		15	1		4		2			9	5			2	16	11		9
# mutation	2	3		13	1		4		2			11	5			2	17	14		16
nonsynonymous SNV	2	2		10			3		1			8	5			2	12	12		11
synonymous SNV		1		3	1		1		1			3					5	2		5

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])

Top

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
chr10:18828550	p.R572H,CACNB2	3
chr10:18828493	p.R553H,CACNB2	2
chr10:18828191	p.A285T,CACNB2	1
chr10:18690886	p.D383N,CACNB2	1
chr10:18807318	p.K472T,CACNB2	1
chr10:18828395	p.R591R,CACNB2	1
chr10:18787377	p.D36Y,CACNB2	1
chr10:18823141	p.S142S,CACNB2	1
chr10:18827198	p.A297A,CACNB2	1
chr10:18795465	p.H397Q,CACNB2	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 CACNB2 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]

Top

Gene Expression for CACNB2

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


BAI2,CACNB2,CARTPT,CDHR3,CNKSR3,CPE,DCLK1, DDX25,FGF10,GPRIN3,GRIK1,IQSEC2,UNC79,LRP2, LRRN4,MAST4,NTRK2,PCSK1,SIAH3,SLC1A2,SYT4	ADAMTS3,CACNB2,CBLN4,CHIC1,CYP3A7,DNAJC18,DZIP1, FKBP7,IFT80,LOC399959,LRRC49,LTBP1,MEIS1,NAP1L3, OGN,PAPPA,PROS1,SEMA3D,TRPC1,ZC3H12B,ZDHHC15

ARG1,AVPR1A,CACNB2,CLEC4D,CXCR1,SUPT20HL2,IL7R, LINGO4,MGAM,MRGPRE,NAIP,NHSL2,OR2T12,PGLYRP1, PREX2,RPH3A,SELE,TCTE1,THSD7A,TNC,WNK3	ANO6,BOK,TMEM245,CACNB2,DCLK2,DDHD2,ECM2, CCSER2,FZD7,GRB10,HOXA4,MTUS2,NAB2,SPACA6P, RGS5,SEC22C,SESTD1,STK33,TPPP3,TRNP1,TRPC1

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

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

Top

Pharmacological Information for CACNB2

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
DB00270	calcium channel, voltage-dependent, beta 2 subunit	approved	Isradipine
DB00381	calcium channel, voltage-dependent, beta 2 subunit	approved	Amlodipine
DB00393	calcium channel, voltage-dependent, beta 2 subunit	approved	Nimodipine
DB00401	calcium channel, voltage-dependent, beta 2 subunit	approved	Nisoldipine
DB00622	calcium channel, voltage-dependent, beta 2 subunit	approved	Nicardipine
DB00653	calcium channel, voltage-dependent, beta 2 subunit	approved	Magnesium Sulfate
DB00661	calcium channel, voltage-dependent, beta 2 subunit	approved	Verapamil
DB01023	calcium channel, voltage-dependent, beta 2 subunit	approved; investigational	Felodipine
DB01054	calcium channel, voltage-dependent, beta 2 subunit	approved	Nitrendipine
DB01115	calcium channel, voltage-dependent, beta 2 subunit	approved	Nifedipine
DB01388	calcium channel, voltage-dependent, beta 2 subunit	withdrawn	Mibefradil
DB06712	calcium channel, voltage-dependent, beta 2 subunit	approved	Nilvadipine

Top

Cross referenced IDs for CACNB2

* 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