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 CA12
Basic gene info.Gene symbolCA12
Gene namecarbonic anhydrase XII
SynonymsCAXII|HsT18816
CytomapUCSC genome browser: 15q22
Genomic locationchr15 :63615729-63674075
Type of geneprotein-coding
RefGenesNM_001218.4,
NM_001293642.1,NM_206925.2,
Ensembl idENSG00000074410
DescriptionCA-XIIcarbonate dehydratase XIIcarbonic anhydrase 12carbonic dehydratasetumor antigen HOM-RCC-3.1.3
Modification date20141207
dbXrefs MIM : 603263
HGNC : HGNC
HPRD : 04464
ProteinUniProt: O43570
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CA12
BioGPS: 771
Gene Expression Atlas: ENSG00000074410
The Human Protein Atlas: ENSG00000074410
PathwayNCI Pathway Interaction Database: CA12
KEGG: CA12
REACTOME: CA12
ConsensusPathDB
Pathway Commons: CA12
MetabolismMetaCyc: CA12
HUMANCyc: CA12
RegulationEnsembl's Regulation: ENSG00000074410
miRBase: chr15 :63,615,729-63,674,075
TargetScan: NM_001218
cisRED: ENSG00000074410
ContextiHOP: CA12
cancer metabolism search in PubMed: CA12
UCL Cancer Institute: CA12
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CA12 in cancer cell metabolism1. Wykoff CC, Beasley NJ, Watson PH, Turner KJ, Pastorek J, et al. (2000) Hypoxia-inducible expression of tumor-associated carbonic anhydrases. Cancer Res 60: 7075-7083. go to article
2. Tozlu S, Girault I, Vacher S, Vendrell J, Andrieu C, et al. (2006) Identification of novel genes that co-cluster with estrogen receptor alpha in breast tumor biopsy specimens, using a large-scale real-time reverse transcription-PCR approach. Endocr Relat Cancer 13: 1109-1120. doi: 10.1677/erc.1.01120. go to article

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Phenotypic Information for CA12(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CA12
Familial Cancer Database: CA12
* 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 143860; phenotype.
603263; gene.
Orphanet
DiseaseKEGG Disease: CA12
MedGen: CA12 (Human Medical Genetics with Condition)
ClinVar: CA12
PhenotypeMGI: CA12 (International Mouse Phenotyping Consortium)
PhenomicDB: CA12

Mutations for CA12
* 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
There's no inter-chromosomal structural variation.
- 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
pancreasCA12chr156364001063640030chr159671214096712160
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 CA12 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AL050025AP1G142803167177618571805102CA1227983994156361573363616925
AI343531RPL32111631287753912877654CA12112446156361752663618065
AI478632CA121343156361971663620058CA12339512156361957563619748
BQ325609MTPN181587135613319135613459CA12154282156361723663617364
CA312936CA1218352156361573063616064CA12346410156361629463616358

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 # sample1                
GAIN (# sample)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=21)
Stat. for Synonymous SNVs
(# total SNVs=16)
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
chr15:63631040-63631040p.L284L2
chr15:63667866-63667866p.T33A2
chr15:63632566-63632566p.G223V1
chr15:63634235-63634235p.S164L1
chr15:63638802-63638802p.L71L1
chr15:63631039-63631039p.V285I1
chr15:63632569-63632569p.R222Q1
chr15:63634241-63634241p.N162S1
chr15:63638846-63638846p.P57S1
chr15:63632575-63632575p.R220H1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 62 1 1  321 131 7
# mutation11 62 1 1  321 131 7
nonsynonymous SNV1  32 1 1  121  3  1
synonymous SNV 1 3       2   1 1 6
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
chr15:63632949p.F80F,CA121
chr15:63638807p.C199C,CA121
chr15:63631115p.L60M,CA121
chr15:63632965p.P172T,CA121
chr15:63638846p.R52H,CA121
chr15:63632540p.P168P,CA121
chr15:63634235p.P41H,CA121
chr15:63638889p.S164S,CA121
chr15:63632550p.L71L,CA121
chr15:63634241p.G163V,CA121

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 CA12 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 CA12

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

AAGAB,ABCD3,ANXA9,APH1B,BBS4,CA12,CELSR1,
CSNK1G1,DIS3L,ESR1,FBXL5,GATA3,PTPLAD1,RAB11A,
SIN3A,SKP1,SLC24A1,SNX1,TBC1D9,THSD4,XBP1
ABAT,ARSD,CA12,CDH1,CELSR1,GOLM1,HHAT,
MARVELD2,MBOAT1,MTL5,MYB,PIP4K2C,PRRG4,SHROOM3,
SLC39A6,TBC1D9,TPBG,TTC8,XBP1,ZNF544,ZNF552

AOC1,ACVRL1,ALDH1L1,CA12,CASP7,CES3,CLRN3,
EHHADH,GPA33,IQGAP2,ITM2C,LIMA1,NOSTRIN,PAPSS2,
PIGR,PLA2G10,RETSAT,TCF7L2,TSPAN1,TSPAN8,VSIG2
ABCC3,AHCYL2,CA12,CNNM4,DSG2,FA2H,FBXO34,
KLF4,LETM1,NCEH1,PLCE1,PPM1B,PPP1R14C,SATB2,
SH3BGRL2,SLC35D1,SLC44A1,SLC4A4,TMEM63B,TMEM65,ZBTB7C
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 CA12
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB O43570; -.
ChemistryChEMBL CHEMBL3242; -.
ChemistryGuidetoPHARMACOLOGY 2747; -.
Organism-specific databasesPharmGKB PA25987; -.
Organism-specific databasesCTD 771; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00562carbonic anhydrase XIIapprovedBenzthiazide
DB00774carbonic anhydrase XIIapprovedHydroflumethiazide
DB00909carbonic anhydrase XIIapproved; investigationalZonisamide
DB00999carbonic anhydrase XIIapprovedHydrochlorothiazide


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Cross referenced IDs for CA12
* 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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