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 CA5B
Basic gene info.Gene symbolCA5B
Gene namecarbonic anhydrase VB, mitochondrial
SynonymsCA-VB
CytomapUCSC genome browser: Xp21.1
Genomic locationchrX :15756411-15805748
Type of geneprotein-coding
RefGenesNM_007220.3,
Ensembl idENSG00000169239
Descriptioncarbonate dehydratase VBcarbonic anhydrase 5B, mitochondrialcarbonic dehydratase
Modification date20141207
dbXrefs MIM : 300230
HGNC : HGNC
Ensembl : ENSG00000169239
HPRD : 02207
Vega : OTTHUMG00000021183
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CA5B
BioGPS: 11238
Gene Expression Atlas: ENSG00000169239
The Human Protein Atlas: ENSG00000169239
PathwayNCI Pathway Interaction Database: CA5B
KEGG: CA5B
REACTOME: CA5B
ConsensusPathDB
Pathway Commons: CA5B
MetabolismMetaCyc: CA5B
HUMANCyc: CA5B
RegulationEnsembl's Regulation: ENSG00000169239
miRBase: chrX :15,756,411-15,805,748
TargetScan: NM_007220
cisRED: ENSG00000169239
ContextiHOP: CA5B
cancer metabolism search in PubMed: CA5B
UCL Cancer Institute: CA5B
Assigned class in ccmGDBC

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Phenotypic Information for CA5B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CA5B
Familial Cancer Database: CA5B
* 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_NITROGEN_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CA5B
MedGen: CA5B (Human Medical Genetics with Condition)
ClinVar: CA5B
PhenotypeMGI: CA5B (International Mouse Phenotyping Consortium)
PhenomicDB: CA5B

Mutations for CA5B
* 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 CA5B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB286696LOC1005074121152?112030112179CA5B152478X1575643215782786

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=21)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr23:15800751-15800751p.A306A4
chr23:15800620-15800620p.R263W2
chr23:15800626-15800626p.L265L2
chr23:15794997-15794997p.?1
chr23:15768234-15768234p.P30A1
chr23:15792463-15792463p.N166N1
chr23:15768283-15768283p.R46L1
chr23:15792482-15792482p.E173K1
chr23:15782766-15782766p.R70W1
chr23:15792527-15792527p.?1

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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   1    2  32   32 6
# mutation   1    2  32   32 6
nonsynonymous SNV   1    2  32   11 5
synonymous SNV                21 1
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
chrX:15794840p.A208T2
chrX:15794885p.Y37F1
chrX:15768234p.R46L1
chrX:15794933p.R70W1
chrX:15768256p.P78L1
chrX:15794942p.V95V1
chrX:15768283p.T144T1
chrX:15800702p.K195N1
chrX:15782766p.D198D1
chrX:15800723p.T223A1

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 CA5B 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 CA5B

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

ATXN1,BMPR2,CA5B,CDKL5,DDX3X,FNIP2,FOXN3,
FZD4,HEG1,HIPK1,INE2,LIMA1,MYO1B,PRKG1,
RSBN1,SLC30A4,SNTB2,SNX30,TGFBR1,ZEB1,ZNF699
AKT3,BBS7,CA5B,CNTLN,CSGALNACT2,EIF5A2,EVI5,
HAUS2,IDS,KCNT2,OMD,RBMS1,RP2,SGMS2,
SLC37A3,STK38L,TBC1D12,TRDMT1,TRPC1,TULP3,UST

ARHGEF6,THEMIS2,CEP85L,CA5B,CSGALNACT2,CXCR4,DZIP1L,
FAM160B1,FAM19A2,FAM49A,HCFC2,LEPR,LIX1L,LRRC8C,
RAB8B,RASSF2,SETBP1,SYNE1,TCP11L2,TSHZ2,ZFX
BEAN,CA5B,CD34,CPE,CYTH3,ECM2,EFHD1,
FGF14,IGFBP6,LEPR,LIFR,MAMDC2,MAP1LC3C,OMD,
PLCXD3,SHISA3,SLC13A3,SLC7A2,TFPI,TMEM204,UST
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 CA5B
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
DB00909carbonic anhydrase VB, mitochondrialapproved; investigationalZonisamide


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Cross referenced IDs for CA5B
* 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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