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 CACNB2
Basic gene info.Gene symbolCACNB2
Gene namecalcium channel, voltage-dependent, beta 2 subunit
SynonymsCACNLB2|CAVB2|MYSB
CytomapUCSC genome browser: 10p12
Genomic locationchr10 :18429605-18830688
Type of geneprotein-coding
RefGenesNM_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 idENSG00000165995
DescriptionCAB2calcium 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 date20141219
dbXrefs MIM : 600003
HGNC : HGNC
Ensembl : ENSG00000165995
HPRD : 02473
Vega : OTTHUMG00000017764
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CACNB2
BioGPS: 783
Gene Expression Atlas: ENSG00000165995
The Human Protein Atlas: ENSG00000165995
PathwayNCI Pathway Interaction Database: CACNB2
KEGG: CACNB2
REACTOME: CACNB2
ConsensusPathDB
Pathway Commons: CACNB2
MetabolismMetaCyc: CACNB2
HUMANCyc: CACNB2
RegulationEnsembl's Regulation: ENSG00000165995
miRBase: chr10 :18,429,605-18,830,688
TargetScan: NM_000724
cisRED: ENSG00000165995
ContextiHOP: CACNB2
cancer metabolism search in PubMed: CACNB2
UCL Cancer Institute: CACNB2
Assigned class in ccmGDBC

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Phenotypic Information for CACNB2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CACNB2
MedGen: CACNB2 (Human Medical Genetics with Condition)
ClinVar: CACNB2
PhenotypeMGI: CACNB2 (International Mouse Phenotyping Consortium)
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.

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
ovaryCACNB2chr101876592518765945chr103243858632438606
ovaryCACNB2chr101878636818786388CACNB2chr101878752418787544
pancreasCACNB2chr101877155918771579CACNB2chr101877278618772806
prostateCACNB2chr101877584318775843chr10111523505111523505
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 CACNB2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA505169MAP912024156297921156298122CACNB2199515101880244918834460
CB962120CACNB21413101849994718500360SPARCL140261248840154188403655
BF222031KLK31172195136384951364020CACNB2171248101848407918484156
BQ380638PTPRK25466128407537128407558CACNB24570101867999618680030
BF921318CACNB221321101882724618828413NUP983135531137930583797143
BF922976CACNB25320101882724618828431NUP983125861137930583797177
AW005394CACNB25183101882077818822031PCGF2181638173689460536895928

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 # sample5       1 4   1 1
GAIN (# sample)5       1 1     1
LOSS (# sample)          3   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=4

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check002.gifSomatic 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)

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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
chr10:18828550-18828550p.R572H4
chr10:18828421-18828421p.S529L3
chr10:18828493-18828493p.R553H3
chr10:18828510-18828510p.R559R3
chr10:18828645-18828645p.R604C2
chr10:18690935-18690935p.A44G2
chr10:18690937-18690937p.E45K2
chr10:18827148-18827148p.D393N2
chr10:18787404-18787404p.E97K2
chr10:18828607-18828607p.R591Q2

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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
# sample23 151 4 2  95  21611 9
# mutation23 131 4 2  115  21714 16
nonsynonymous SNV22 10  3 1  85  21212 11
synonymous SNV 1 31 1 1  3    52 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])

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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
chr10:18828550p.R572H,CACNB23
chr10:18828493p.R553H,CACNB22
chr10:18690892p.A481T,CACNB21
chr10:18816561p.E45K,CACNB21
chr10:18828215p.P165H,CACNB21
chr10:18789754p.L309H,CACNB21
chr10:18825082p.T409T,CACNB21
chr10:18803206p.R487H,CACNB21
chr10:18827213p.L52L,CACNB21
chr10:18690910p.D171D,CACNB21

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 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]

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Gene Expression for CACNB2

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

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
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 CACNB2
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
DB00270calcium channel, voltage-dependent, beta 2 subunitapprovedIsradipine
DB00381calcium channel, voltage-dependent, beta 2 subunitapprovedAmlodipine
DB00393calcium channel, voltage-dependent, beta 2 subunitapprovedNimodipine
DB00401calcium channel, voltage-dependent, beta 2 subunitapprovedNisoldipine
DB00622calcium channel, voltage-dependent, beta 2 subunitapprovedNicardipine
DB00653calcium channel, voltage-dependent, beta 2 subunitapprovedMagnesium Sulfate
DB00661calcium channel, voltage-dependent, beta 2 subunitapprovedVerapamil
DB01023calcium channel, voltage-dependent, beta 2 subunitapproved; investigationalFelodipine
DB01054calcium channel, voltage-dependent, beta 2 subunitapprovedNitrendipine
DB01115calcium channel, voltage-dependent, beta 2 subunitapprovedNifedipine
DB01388calcium channel, voltage-dependent, beta 2 subunitwithdrawnMibefradil
DB06712calcium channel, voltage-dependent, beta 2 subunitapprovedNilvadipine


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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



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