Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	CA12
	Gene name	carbonic anhydrase XII
	Synonyms	CAXII\|HsT18816
	Cytomap	UCSC genome browser: 15q22
	Genomic location	chr15 :63615729-63674075
	Type of gene	protein-coding
	RefGenes	NM_001218.4, NM_001293642.1,NM_206925.2,
	Ensembl id	ENSG00000074410
	Description	CA-XIIcarbonate dehydratase XIIcarbonic anhydrase 12carbonic dehydratasetumor antigen HOM-RCC-3.1.3
	Modification date	20141207
dbXrefs	MIM : 603263
	HGNC : HGNC
	HPRD : 04464
Protein	UniProt: O43570 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CA12
	BioGPS: 771
	Gene Expression Atlas: ENSG00000074410
	The Human Protein Atlas: ENSG00000074410
Pathway	NCI Pathway Interaction Database: CA12
	KEGG: CA12
	REACTOME: CA12
	ConsensusPathDB
	Pathway Commons: CA12
Metabolism	MetaCyc: CA12
	HUMANCyc: CA12
Regulation	Ensembl's Regulation: ENSG00000074410
	miRBase: chr15 :63,615,729-63,674,075
	TargetScan: NM_001218
	cisRED: ENSG00000074410
Context	iHOP: CA12
	cancer metabolism search in PubMed: CA12
	UCL Cancer Institute: CA12
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CA12 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_NITROGEN_METABOLISM

Others
OMIM	143860; phenotype. 603263; gene.
Orphanet
Disease	KEGG Disease: CA12
	MedGen: CA12 (Human Medical Genetics with Condition)
	ClinVar: CA12
Phenotype	MGI: CA12 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	CA12	chr15	63640010	63640030		chr15	96712140	96712160

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CA12 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
AL050025	AP1G1	4	2803	16	71776185	71805102	CA12	2798	3994	15	63615733	63616925
AI343531	RPL32	1	116	3	12877539	12877654	CA12	112	446	15	63617526	63618065
AI478632	CA12	1	343	15	63619716	63620058	CA12	339	512	15	63619575	63619748
BQ325609	MTPN	18	158	7	135613319	135613459	CA12	154	282	15	63617236	63617364
CA312936	CA12	18	352	15	63615730	63616064	CA12	346	410	15	63616294	63616358

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr15:63667866-63667866	p.T33A	2
chr15:63631040-63631040	p.L284L	2
chr15:63632575-63632575	p.R220H	1
chr15:63634277-63634277	p.N150T	1
chr15:63631051-63631051	p.D281N	1
chr15:63638889-63638889	p.S42S	1
chr15:63632589-63632589	p.T215T	1
chr15:63637684-63637684	p.A141T	1
chr15:63631087-63631087	p.E269*	1
chr15:63632593-63632593	p.R214K	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		6	2		1		1			3	2	1		1	3	1		7
# mutation	1	1		6	2		1		1			3	2	1		1	3	1		7
nonsynonymous SNV	1			3	2		1		1			1	2	1			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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr15:63634235	p.R154K,CA12	1
chr15:63638889	p.S70R,CA12	1
chr15:63632550	p.F145F,CA12	1
chr15:63634241	p.P57S,CA12	1
chr15:63632562	p.P143P,CA12	1
chr15:63634277	p.S42S,CA12	1
chr15:63632566	p.V142I,CA12	1
chr15:63637684	p.L130L,CA12	1
chr15:63618489	p.A283T,CA12	1
chr15:63632593	p.F127L,CA12	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	O43570; -.
Chemistry	ChEMBL	CHEMBL3242; -.
Chemistry	GuidetoPHARMACOLOGY	2747; -.
Organism-specific databases	PharmGKB	PA25987; -.
Organism-specific databases	CTD	771; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00562	carbonic anhydrase XII	approved	Benzthiazide
DB00774	carbonic anhydrase XII	approved	Hydroflumethiazide
DB00909	carbonic anhydrase XII	approved; investigational	Zonisamide
DB00999	carbonic anhydrase XII	approved	Hydrochlorothiazide

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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