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 CA7
Basic gene info.Gene symbolCA7
Gene namecarbonic anhydrase VII
SynonymsCAVII
CytomapUCSC genome browser: 16q22.1
Genomic locationchr16 :66878840-66888049
Type of geneprotein-coding
RefGenesNM_001014435.1,
NM_005182.2,
Ensembl idENSG00000168748
DescriptionCA-VIIcarbonate dehydratase VIIcarbonic anhydrase 7carbonic dehydratase VII
Modification date20141207
dbXrefs MIM : 114770
HGNC : HGNC
Ensembl : ENSG00000168748
HPRD : 00263
Vega : OTTHUMG00000137524
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CA7
BioGPS: 766
Gene Expression Atlas: ENSG00000168748
The Human Protein Atlas: ENSG00000168748
PathwayNCI Pathway Interaction Database: CA7
KEGG: CA7
REACTOME: CA7
ConsensusPathDB
Pathway Commons: CA7
MetabolismMetaCyc: CA7
HUMANCyc: CA7
RegulationEnsembl's Regulation: ENSG00000168748
miRBase: chr16 :66,878,840-66,888,049
TargetScan: NM_001014435
cisRED: ENSG00000168748
ContextiHOP: CA7
cancer metabolism search in PubMed: CA7
UCL Cancer Institute: CA7
Assigned class in ccmGDBC

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Phenotypic Information for CA7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CA7
Familial Cancer Database: CA7
* 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: CA7
MedGen: CA7 (Human Medical Genetics with Condition)
ClinVar: CA7
PhenotypeMGI: CA7 (International Mouse Phenotyping Consortium)
PhenomicDB: CA7

Mutations for CA7
* 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 CA7 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
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=14)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr16:66880978-66880978p.R29H2
chr16:66885451-66885451p.L150fs*102
chr16:66887326-66887326p.R240S2
chr16:66881124-66881124p.R78*2
chr16:66884460-66884460p.P85P2
chr16:66885423-66885423p.A139S2
chr16:66886742-66886742p.R215Q1
chr16:66887311-66887311p.S235S1
chr16:66881002-66881002p.S37Y1
chr16:66885454-66885454p.F149Y1

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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
# sample11 4  1 3  12   13 4
# mutation11 4  1 2  12   13 4
nonsynonymous SNV   3    2   2   12 4
synonymous SNV11 1  1 1  1     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
chr16:66880978p.A83S,CA72
chr16:66887326p.R184S,CA72
chr16:66885423p.R29H2
chr16:66885594p.S37Y1
chr16:66885607p.L3L,CA71
chr16:66881002p.N17N,CA71
chr16:66886638p.G27G,CA71
chr16:66881069p.H68H,CA71
chr16:66886682p.N70K,CA71
chr16:66881111p.E95G,CA71

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 CA7 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 CA7

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

SERTM1,C1orf110,TSPEAR,FAXDC2,CA7,EVX1,FAM105A,
BRINP2,GABRR3,GALNT3,KLHL14,NCAM1,PCDH19,PDZRN4,
SATB1,SLC13A4,SLC14A2,SLC26A2,SLC44A5,TSPAN19,VWA3A
C10orf99,C16orf92,C9orf84,CA7,CALML3,CCL27,DEFB109P1B,
HMGB4,IL36A,KRT13,KRT84,KRTAP15-1,OR10G8,OR1F1,
OR4P4,OTOP3,PPY,SCARNA27,SPRR3,TMPRSS11A,UGT2A1

C1QTNF8,C4orf51,CA7,CCL26,CRYBA4,GJA3,HELT,
ISYNA1,KRT3,LAG3,NXPH4,TINCR,PPM1K,PRAMEF6,
PRB1,PRB2,PRR4,RXFP2,TRIM69,PRSS58,WDR11
ATG4B,BEST4,CA1,CA7,CAPN13,CEACAM3,ENDOD1,
FKBP1A,GGA1,GIPR,MROH1,ITM2C,KLF4,OTOP2,
PARM1,SPIB,ST6GALNAC6,TFCP2L1,TMEM72,TTLL6,UNC5C
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 CA7
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
DB00311carbonic anhydrase VIIapprovedEthoxzolamide
DB00703carbonic anhydrase VIIapprovedMethazolamide
DB00819carbonic anhydrase VIIapprovedAcetazolamide
DB00909carbonic anhydrase VIIapproved; investigationalZonisamide
DB01144carbonic anhydrase VIIapprovedDichlorphenamide


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Cross referenced IDs for CA7
* 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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