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 CANT1

Basic gene info.	Gene symbol	CANT1
	Gene name	calcium activated nucleotidase 1
	Synonyms	DBQD\|SCAN-1\|SCAN1\|SHAPY
	Cytomap	UCSC genome browser: 17q25.3
	Genomic location	chr17 :76987797-77005899
	Type of gene	protein-coding
	RefGenes	NM_001159772.1, NM_001159773.1,NM_138793.3,
	Ensembl id	ENSG00000171302
	Description	Ca2+-dependent endoplasmic reticulum nucleoside diphosphataseapyrase homologmicromelic dwarfism with vertebral and metaphyseal abnormalities and advanced carpotarsal ossificationputative MAPK-activating protein PM09putative NF-kappa-B-activating prote
	Modification date	20141207
dbXrefs	MIM : 613165
	HGNC : HGNC
	Ensembl : ENSG00000171302
	HPRD : 13003
	Vega : OTTHUMG00000177570
Protein	UniProt: Q8WVQ1 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CANT1
	BioGPS: 124583
	Gene Expression Atlas: ENSG00000171302
	The Human Protein Atlas: ENSG00000171302
Pathway	NCI Pathway Interaction Database: CANT1
	KEGG: CANT1
	REACTOME: CANT1
	ConsensusPathDB
	Pathway Commons: CANT1
Metabolism	MetaCyc: CANT1
	HUMANCyc: CANT1
Regulation	Ensembl's Regulation: ENSG00000171302
	miRBase: chr17 :76,987,797-77,005,899
	TargetScan: NM_001159772
	cisRED: ENSG00000171302
Context	iHOP: CANT1
	cancer metabolism search in PubMed: CANT1
	UCL Cancer Institute: CANT1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CANT1 in cancer cell metabolism	1. Gerhardt J, Steinbrech C, Buchi O, Behnke S, Bohnert A, et al. (2011) The androgen-regulated Calcium-Activated Nucleotidase 1 (CANT1) is commonly overexpressed in prostate cancer and is tumor-biologically relevant in vitro. Am J Pathol 178: 1847-1860. doi: 10.1016/j.ajpath.2010.12.046. pmid: 3078458 go to article

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Phenotypic Information for CANT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CANT1
	Familial Cancer Database: CANT1

* 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_PURINE_METABOLISM KEGG_PYRIMIDINE_METABOLISM

Others
OMIM	251450; phenotype. 613165; gene.
Orphanet	1425; Desbuquois syndrome.
Disease	KEGG Disease: CANT1
	MedGen: CANT1 (Human Medical Genetics with Condition)
	ClinVar: CANT1
Phenotype	MGI: CANT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CANT1

Mutations for CANT1

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CANT1 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
EU693078	CANT1	1	128	17	77001454	77001581	ETV4	127	389	17	41610637	41613849
BE816214	CANT1	1	211	17	76988787	76988997	CANT1	209	277	17	76989012	76989080

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

There's no copy number variation information in COSMIC data for this gene.

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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=26)	Stat. for Synonymous SNVs (# total SNVs=19)

Stat. for Deletions (# total SNVs=2)	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
chr17:76993423-76993423	p.S94S	2
chr17:76993313-76993313	p.K131R	2
chr17:76993507-76993507	p.G67fs*63	2
chr17:76989644-76989644	p.I398M	2
chr17:76991114-76991114	p.G274A	2
chr17:76993522-76993522	p.S61S	2
chr17:76993169-76993169	p.S179F	2
chr17:76993539-76993539	p.L56F	2
chr17:76991166-76991166	p.V257M	2
chr17:76989736-76989737	p.G368fs*>35	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=2

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	2	1	6	1		2					5	5	1			10	4		5
# mutation	1	2	1	6	1		2					5	5	1			9	4		7
nonsynonymous SNV		1		3	1							3	3	1			7	4		1
synonymous SNV	1	1	1	3			2					2	2				2			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
chr17:76993522	p.S61S,CANT1	2
chr17:76993539	p.L56F,CANT1	2
chr17:76989755	p.F349L,CANT1	1
chr17:76993507	p.S179F,CANT1	1
chr17:76991155	p.L59P,CANT1	1
chr17:76993257	p.G343D,CANT1	1
chr17:76989776	p.G175W,CANT1	1
chr17:76993512	p.G343R,CANT1	1
chr17:76991172	p.N174N,CANT1	1
chr17:76993275	p.T48T,CANT1	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 CANT1 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 CANT1

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


BAIAP2,HID1,C17orf80,CANT1,COG1,CSNK1D,DNAJA4, DYNLL2,KCTD2,KIAA0195,LLGL2,MIF4GD,MTMR4,PBX1, RNF43,RPTOR,SLC26A11,SLC27A4,SLC9A3R1,SYNGR2,TBCD	AP1M2,ARHGAP39,CANT1,CDH1,CRB3,CREB3L4,DLG3, ERBB3,FAM83H,FKBP4,GOLM1,ILDR1,KIAA1324,CAMSAP3, MAPK13,MARVELD2,RAB11FIP4,SEZ6L2,SHROOM2,SPDEF,TJP3

BACE2,HID1,TMEM246,CANT1,CDC42EP4,CREB3L1,FAM57A, FOXA3,FUT8,FFAR4,LRP10,MLPH,P4HB,PTGER2, SERPINB1,SGPP2,SH2D4A,ST6GALNAC1,VPS37B,VWA3B,ZBTB7C	ACVRL1,APH1A,CANT1,CDC42EP5,CDX1,DHX32,GALNT12, GIPC1,GUSB,ILDR1,IMPA2,ITM2C,LIMK2,LLGL2, LSR,MAGIX,MARCH3,OVOL2,RHBDL2,TMPRSS4,TOR2A

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 CANT1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA134984439; -.
Organism-specific databases	CTD	124583; -.

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
DB03486	calcium activated nucleotidase 1	experimental	Phosphomethylphosphonic Acid Guanosyl Ester
DB03754	calcium activated nucleotidase 1	experimental	Tris(Hydroxymethyl)Aminomethane

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Cross referenced IDs for CANT1

* 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