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 CA1
Basic gene info.Gene symbolCA1
Gene namecarbonic anhydrase I
SynonymsCA-I|CAB|Car1|HEL-S-11
CytomapUCSC genome browser: 8q21.2
Genomic locationchr8 :86240457-86253943
Type of geneprotein-coding
RefGenesNM_001128829.3,
NM_001128830.3,NM_001128831.3,NM_001164830.1,NM_001291967.1,
NM_001291968.1,NM_001738.4,
Ensembl idENSG00000133742
Descriptioncarbonate dehydratase Icarbonic anhydrase 1carbonic anhydrase Bepididymis secretory protein Li 11
Modification date20141207
dbXrefs MIM : 114800
HGNC : HGNC
Ensembl : ENSG00000133742
HPRD : 00265
Vega : OTTHUMG00000164941
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CA1
BioGPS: 759
Gene Expression Atlas: ENSG00000133742
The Human Protein Atlas: ENSG00000133742
PathwayNCI Pathway Interaction Database: CA1
KEGG: CA1
REACTOME: CA1
ConsensusPathDB
Pathway Commons: CA1
MetabolismMetaCyc: CA1
HUMANCyc: CA1
RegulationEnsembl's Regulation: ENSG00000133742
miRBase: chr8 :86,240,457-86,253,943
TargetScan: NM_001128829
cisRED: ENSG00000133742
ContextiHOP: CA1
cancer metabolism search in PubMed: CA1
UCL Cancer Institute: CA1
Assigned class in ccmGDBC

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Phenotypic Information for CA1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CA1
Familial Cancer Database: CA1
* 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: CA1
MedGen: CA1 (Human Medical Genetics with Condition)
ClinVar: CA1
PhenotypeMGI: CA1 (International Mouse Phenotyping Consortium)
PhenomicDB: CA1

Mutations for CA1
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryCA1chr88625275686252776chr121985467819854698
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 CA1 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      
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=30)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr8:86250541-86250541p.E59*3
chr8:86249257-86249257p.L91F2
chr8:86244737-86244737p.L165L2
chr8:86250640-86250640p.G26R2
chr8:86240852-86240852p.M242fs*111
chr8:86249251-86249251p.Q93*1
chr8:86242016-86242016p.D191H1
chr8:86250523-86250524p.H65fs*81
chr8:86244781-86244781p.V151I1
chr8:86253848-86253848p.W6*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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 1  1 1  8 1 192 6
# mutation 2 1  1 1  8 1 192 6
nonsynonymous SNV 1 1  1    5 1  71 4
synonymous SNV 1      1  3   121 2
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
chr8:86241982p.F67C,CA11
chr8:86245775p.E72K,CA11
chr8:86250633p.P63P,CA11
chr8:86242016p.F71V,CA11
chr8:86245846p.A62A,CA11
chr8:86250640p.T56A,CA11
chr8:86242048p.K60E,CA11
chr8:86249177p.T43T,CA11
chr8:86250676p.L52P,CA11
chr8:86242059p.N28T,CA11

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 CA1 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 CA1

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

ABHD12,ABHD14A,ADIRF,CA14,CYB5D2,DUSP15,EML2,
FLJ45983,HPN,LOC100190938,LOC284276,NDUFS8,NHLRC4,NPRL2,
OR5M3,OR5M8,OR5R1,P4HTM,SERPINI1,SFXN2,TEX264
RBFOX1,AMPD1,ANKRD23,ASB16,ASB4,ASB5,CA14,
CACNG1,CALML6,CAPN3,CLCN1,CMYA5,FITM1,JPH1,
MYOZ3,OBSCN,PFKM,RYR1,SRPK3,TMEM38A,UCP3

ABCA7,ABCC11,ASIC3,ARMC7,CA14,CLCN1,CSTB,
DGKA,DMBX1,ENDOV,KIF14,LOC100131691,OR4C3,PRICKLE4,
ROPN1B,RUSC1,SLC44A2,SLC45A3,SLC47A2,SNX24,TDRD12
ASIC1,ARHGEF4,ATP1A2,BVES,NPR3,CA14,CAMK2G,
DACT3,DNAJB5,KCTD8,KY,LDB3,MYOM1,PDLIM7,
PLCD4,PNCK,PYGM,SMTN,TGFB1I1,THBS4,TPM2
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 CA1
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 IapprovedMethyclothiazide
DB00311carbonic anhydrase IapprovedEthoxzolamide
DB00381carbonic anhydrase IapprovedAmlodipine
DB00423carbonic anhydrase IapprovedMethocarbamol
DB00436carbonic anhydrase IapprovedBendroflumethiazide
DB00562carbonic anhydrase IapprovedBenzthiazide
DB00606carbonic anhydrase IapprovedCyclothiazide
DB00703carbonic anhydrase IapprovedMethazolamide
DB00774carbonic anhydrase IapprovedHydroflumethiazide
DB00819carbonic anhydrase IapprovedAcetazolamide
DB00869carbonic anhydrase IapprovedDorzolamide
DB00880carbonic anhydrase IapprovedChlorothiazide
DB00909carbonic anhydrase Iapproved; investigationalZonisamide
DB00999carbonic anhydrase IapprovedHydrochlorothiazide
DB01021carbonic anhydrase IapprovedTrichlormethiazide
DB01031carbonic anhydrase Iillicit; approvedEthinamate
DB01119carbonic anhydrase IapprovedDiazoxide
DB01144carbonic anhydrase IapprovedDichlorphenamide
DB01194carbonic anhydrase IapprovedBrinzolamide
DB01325carbonic anhydrase IapprovedQuinethazone
DB08155carbonic anhydrase IexperimentalN-{2-[4-(AMINOSULFONYL)PHENYL]ETHYL}ACETAMIDE
DB08156carbonic anhydrase Iexperimental3-[4-(AMINOSULFONYL)PHENYL]PROPANOIC ACID
DB08157carbonic anhydrase IexperimentalETHYL 3-[4-(AMINOSULFONYL)PHENYL]PROPANOATE


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Cross referenced IDs for CA1
* 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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