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 CA4
Basic gene info.Gene symbolCA4
Gene namecarbonic anhydrase IV
SynonymsCAIV|Car4|RP17
CytomapUCSC genome browser: 17q23
Genomic locationchr17 :58227301-58236906
Type of geneprotein-coding
RefGenesNM_000717.3,
Ensembl idENSG00000167434
DescriptionCA-IVcarbonate dehydratase IVcarbonic anhydrase 4carbonic dehydratase IV
Modification date20141219
dbXrefs MIM : 114760
HGNC : HGNC
Ensembl : ENSG00000167434
HPRD : 00261
Vega : OTTHUMG00000179987
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CA4
BioGPS: 762
Gene Expression Atlas: ENSG00000167434
The Human Protein Atlas: ENSG00000167434
PathwayNCI Pathway Interaction Database: CA4
KEGG: CA4
REACTOME: CA4
ConsensusPathDB
Pathway Commons: CA4
MetabolismMetaCyc: CA4
HUMANCyc: CA4
RegulationEnsembl's Regulation: ENSG00000167434
miRBase: chr17 :58,227,301-58,236,906
TargetScan: NM_000717
cisRED: ENSG00000167434
ContextiHOP: CA4
cancer metabolism search in PubMed: CA4
UCL Cancer Institute: CA4
Assigned class in ccmGDBC

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Phenotypic Information for CA4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CA4
Familial Cancer Database: CA4
* 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: CA4
MedGen: CA4 (Human Medical Genetics with Condition)
ClinVar: CA4
PhenotypeMGI: CA4 (International Mouse Phenotyping Consortium)
PhenomicDB: CA4

Mutations for CA4
* 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 CA4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample   1    1        
GAIN (# sample)   1    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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=16)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr17:58234054-58234054p.T82T2
chr17:58234066-58234066p.N86N2
chr17:58234034-58234034p.D76N1
chr17:58234889-58234889p.K124*1
chr17:58235707-58235708p.R215I1
chr17:58232704-58232704p.E30K1
chr17:58234039-58234039p.K77K1
chr17:58234891-58234891p.K124K1
chr17:58235758-58235758p.K232R1
chr17:58233921-58233921p.V38A1

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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
# sample12 5  4 1  411  74 1
# mutation12 5  4 1  411  74 1
nonsynonymous SNV11 3  4    311  43 1
synonymous SNV 1 2    1  1    31  
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
chr17:58227437p.E30K1
chr17:58234821p.K124K1
chr17:58235472p.V38A1
chr17:58232704p.S129I1
chr17:58234823p.P39A1
chr17:58235480p.G148E1
chr17:58233921p.V40A1
chr17:58234824p.S150S1
chr17:58235657p.V40V1
chr17:58233923p.V170G1

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 CA4 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 CA4

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

AQP7,AQP7P1,ATOH8,BTNL9,C14orf180,CA4,CD300LG,
CLDN5,CRHBP,GLYAT,GPIHBP1,GPR146,HSD17B13,KCNIP2,
LEP,NPR1,PDE2A,PLIN1,RDH5,SDPR,SLC22A12
ABLIM3,BTNL9,CA4,CD300LG,EHD2,GNAZ,GPER1,
GPIHBP1,GPR146,HOXB7,INPP5K,LOC158376,NRN1,PALM,
PTH1R,RBP7,RRAS,ST6GALNAC6,TCF15,VEGFB,VTI1B

ASPG,BTNL3,CA2,CA4,CASP5,CDKN2B-AS1,CEACAM7,
CLCA4,GUCA2A,GUCA2B,MS4A12,SLC51B,OTOP2,SCNN1B,
SEPP1,SLC25A34,SLC26A3,SLC30A10,SLC6A19,TMIGD1,TRIM40
AMACR,ATP1B3,CNPPD1,CA4,CAPN2,CEACAM7,CLCN2,
ABHD17C,GBA,GTPBP2,LITAF,MGLL,P2RX4,PEX26,
PPARG,PRR15,SGK2,SLC26A3,TJP3,TMEM8A,TSPAN1
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 CA4
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
DB00232carbonic anhydrase IVapprovedMethyclothiazide
DB00273carbonic anhydrase IVapproved; investigationalTopiramate
DB00311carbonic anhydrase IVapprovedEthoxzolamide
DB00436carbonic anhydrase IVapprovedBendroflumethiazide
DB00562carbonic anhydrase IVapprovedBenzthiazide
DB00606carbonic anhydrase IVapprovedCyclothiazide
DB00703carbonic anhydrase IVapprovedMethazolamide
DB00774carbonic anhydrase IVapprovedHydroflumethiazide
DB00819carbonic anhydrase IVapprovedAcetazolamide
DB00869carbonic anhydrase IVapprovedDorzolamide
DB00880carbonic anhydrase IVapprovedChlorothiazide
DB00909carbonic anhydrase IVapproved; investigationalZonisamide
DB00999carbonic anhydrase IVapprovedHydrochlorothiazide
DB01021carbonic anhydrase IVapprovedTrichlormethiazide
DB01144carbonic anhydrase IVapprovedDichlorphenamide
DB01194carbonic anhydrase IVapprovedBrinzolamide


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Cross referenced IDs for CA4
* 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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