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 CA9

Basic gene info.	Gene symbol	CA9
	Gene name	carbonic anhydrase IX
	Synonyms	CAIX\|MN
	Cytomap	UCSC genome browser: 9p13.3
	Genomic location	chr9 :35673914-35681154
	Type of gene	protein-coding
	RefGenes	NM_001216.2,
	Ensembl id	ENSG00000107159
	Description	CA-IXP54/58NRCC-associated antigen G250RCC-associated protein G250carbonate dehydratase IXcarbonic anhydrase 9carbonic dehydratasemembrane antigen MNpMW1renal cell carcinoma-associated antigen G250
	Modification date	20141222
dbXrefs	MIM : 603179
	HGNC : HGNC
	Ensembl : ENSG00000107159
	HPRD : 04417
	Vega : OTTHUMG00000021029
Protein	UniProt: Q16790 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CA9
	BioGPS: 768
	Gene Expression Atlas: ENSG00000107159
	The Human Protein Atlas: ENSG00000107159
Pathway	NCI Pathway Interaction Database: CA9
	KEGG: CA9
	REACTOME: CA9
	ConsensusPathDB
	Pathway Commons: CA9
Metabolism	MetaCyc: CA9
	HUMANCyc: CA9
Regulation	Ensembl's Regulation: ENSG00000107159
	miRBase: chr9 :35,673,914-35,681,154
	TargetScan: NM_001216
	cisRED: ENSG00000107159
Context	iHOP: CA9
	cancer metabolism search in PubMed: CA9
	UCL Cancer Institute: CA9
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CA9 in cancer cell metabolism	1. Motzer RJ, Hutson TE, Hudes GR, Figlin RA, Martini JF, et al. (2014) Investigation of novel circulating proteins, germ line single-nucleotide polymorphisms, and molecular tumor markers as potential efficacy biomarkers of first-line sunitinib therapy for advanced renal cell carcinoma. Cancer Chemother Pharmacol 74: 739-750. doi: 10.1007/s00280-014-2539-0. pmid: 4175044 go to article 2. Sheng W, Dong M, Zhou J, Li X, Dong Q (2013) Down regulation of CAII is associated with tumor differentiation and poor prognosis in patients with pancreatic cancer. J Surg Oncol 107: 536-543. doi: 10.1002/jso.23282. go to article 3. Zhou R, Huang W, Yao Y, Wang Y, Li Z, et al. (2013) CA II, a potential biomarker by proteomic analysis, exerts significant inhibitory effect on the growth of colorectal cancer cells. Int J Oncol 43: 611-621. doi: 10.3892/ijo.2013.1972. go to article 4. Riafrecha LE, Rodriguez OM, Vullo D, Supuran CT, Colinas PA (2014) Attachment of carbohydrates to methoxyaryl moieties leads to highly selective inhibitors of the cancer associated carbonic anhydrase isoforms IX and XII. Bioorg Med Chem 22: 5308-5314. doi: 10.1016/j.bmc.2014.07.052. go to article 5. Soltysova A, Breza J, Takacova M, Feruszova J, Hudecova S, et al. (2015) Deregulation of energetic metabolism in the clear cell renal cell carcinoma: A multiple pathway analysis based on microarray profiling. Int J Oncol 47: 287-295. doi: 10.3892/ijo.2015.3014. go to article

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Phenotypic Information for CA9(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CA9
	Familial Cancer Database: CA9

* 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	603179; gene.
Orphanet
Disease	KEGG Disease: CA9
	MedGen: CA9 (Human Medical Genetics with Condition)
	ClinVar: CA9
Phenotype	MGI: CA9 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CA9

Mutations for CA9

* 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
ovary	CA9	chr9	35676861	35676881		chr9	35671879	35671899

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 CA9 related fusion information.

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

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=39)	Stat. for Synonymous SNVs (# total SNVs=11)

Stat. for Deletions (# total SNVs=5)	Stat. for Insertions (# total SNVs=0)
	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
chr9:35674208-35674208	p.P84P	6
chr9:35674191-35674208	p.G79_P84delGEEDLP	5
chr9:35674204-35674204	p.L83P	4
chr9:35674228-35674228	p.G91E	3
chr9:35674151-35674151	p.L65L	2
chr9:35676157-35676157	p.R234H	1
chr9:35674290-35674290	p.D112Y	1
chr9:35679230-35679230	p.S319F	1
chr9:35675828-35675828	p.P168P	1
chr9:35679916-35679916	p.A377A	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=3

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	3		12	1				1			5	1	5		1	7	5		3
# mutation	1	3		12	1				1			5	1	5		1	9	5		3
nonsynonymous SNV	1	3		7	1				1			5	1	3		1	6	4		3
synonymous SNV				5										2			3	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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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
chr9:35674151	p.L65L	2
chr9:35679942	p.S102A	1
chr9:35674227	p.P216R	1
chr9:35675828	p.A392T	1
chr9:35676375	p.D112Y	1
chr9:35679959	p.E249K	1
chr9:35674260	p.E402K	1
chr9:35675906	p.H130N	1
chr9:35677795	p.H251N	1
chr9:35674290	p.V404I	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 CA9 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 CA9

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


ADM,B3GNT4,BNC1,CA9,CSRP2,ENO1,FSCN1, GAPDH,GJB5,GPI,KRT5,KRT75,NDRG1,NMB, PFKP,PKM,S100A2,SLC2A1,TPI1,TUBA1C,TUBA4A	VRTN,C1QTNF8,C7orf33,CA9,CHD5,CLPS,COL9A1, CPNE6,DRP2,HBG1,HBG2,ITLN1,KIF1A,MLC1, NKX2-3,NOBOX,P2RX1,POU5F1B,SOST,WFDC1,ZFP42

ALDOA,CA9,EGLN3,ENO1,ENO2,ERO1L,GAPDH, GBE1,GPI,LDHA,MUC1,P4HA1,PFKP,PGAM1, PKM,PLA2G2A,PNPLA3,RNF183,SLC6A8,SYT8,TBC1D21	ASPDH,TMEM252,CA9,CLDN15,CPS1,DAK,DEFA5, DEFA6,DPEP1,FBP1,GGN,KDM8,KHK,OTC, PDZD7,PRSS1,REG3A,SLC10A2,SULT2B1,TBX3,TTC36

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 CA9

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q16790; -.
Chemistry	ChEMBL	CHEMBL2095180; -.
Organism-specific databases	PharmGKB	PA25998; -.
Organism-specific databases	CTD	768; -.

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 IX	approved	Benzthiazide
DB00774	carbonic anhydrase IX	approved	Hydroflumethiazide
DB00909	carbonic anhydrase IX	approved; investigational	Zonisamide
DB00999	carbonic anhydrase IX	approved	Hydrochlorothiazide

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Cross referenced IDs for CA9

* 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