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 NT5C2

Basic gene info.	Gene symbol	NT5C2
	Gene name	5'-nucleotidase, cytosolic II
	Synonyms	GMP\|NT5B\|PNT5\|SPG45\|SPG65\|cN-II
	Cytomap	UCSC genome browser: 10q24.32
	Genomic location	chr10 :104847773-104953063
	Type of gene	protein-coding
	RefGenes	NM_001134373.2, NM_012229.4,
	Ensembl id	ENSG00000076685
	Description	5'-nucleotidase (purine), cytosolic type BIMP-specific 5'-NTcytosolic 5'-nucleotidase IIcytosolic purine 5'-nucleotidasepurine 5' nucleotidase
	Modification date	20141207
dbXrefs	MIM : 600417
	HGNC : HGNC
	Ensembl : ENSG00000076685
	HPRD : 02686
	Vega : OTTHUMG00000018981
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NT5C2
	BioGPS: 22978
	Gene Expression Atlas: ENSG00000076685
	The Human Protein Atlas: ENSG00000076685
Pathway	NCI Pathway Interaction Database: NT5C2
	KEGG: NT5C2
	REACTOME: NT5C2
	ConsensusPathDB
	Pathway Commons: NT5C2
Metabolism	MetaCyc: NT5C2
	HUMANCyc: NT5C2
Regulation	Ensembl's Regulation: ENSG00000076685
	miRBase: chr10 :104,847,773-104,953,063
	TargetScan: NM_001134373
	cisRED: ENSG00000076685
Context	iHOP: NT5C2
	cancer metabolism search in PubMed: NT5C2
	UCL Cancer Institute: NT5C2
Assigned class in ccmGDB	C

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Phenotypic Information for NT5C2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: NT5C2
	Familial Cancer Database: NT5C2

* 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 KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM REACTOME_ABACAVIR_TRANSPORT_AND_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PURINE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: NT5C2
	MedGen: NT5C2 (Human Medical Genetics with Condition)
	ClinVar: NT5C2
Phenotype	MGI: NT5C2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: NT5C2

Mutations for NT5C2

* 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 NT5C2 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
BE936930	NT5C2	12	139	10	104879475	104879603	NT5C2	136	303	10	104878417	104878583
BE936897	NT5C2	1	169	10	104879430	104879603	NT5C2	157	368	10	104878404	104878617
AW008648	NT5C2	1	135	10	104952890	104953024	NT5C2	126	505	10	104952285	104952664
BE178418	NT5C2	1	305	10	104879460	104879765	NT5C2	301	615	10	104878246	104878560
DA677984	NT5C2	1	285	10	104934614	104953029	SHOC2	284	579	10	112723882	112724177
BE178183	NT5C2	16	319	10	104878246	104878557	NT5C2	315	631	10	104879448	104879765

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=33)	Stat. for Synonymous SNVs (# total SNVs=9)

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
chr10:104852955-104852955	p.R367Q	3
chr10:104934693-104934693	p.R8Q	3
chr10:104859732-104859732	p.R195Q	2
chr10:104866378-104866378	p.L87L	2
chr10:104851364-104851364	p.E390K	2
chr10:104866428-104866428	p.E71K	2
chr10:104854184-104854184	p.S281F	2
chr10:104857052-104857052	p.T256I	1
chr10:104849434-104849434	p.E561K	1
chr10:104850465-104850465	p.A451V	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	2		1	12	1							1	4			1	3	6		8
# mutation	2		1	13	1							1	4			1	3	7		10
nonsynonymous SNV	2		1	8								1	4			1	3	7		7
synonymous SNV				5	1															3

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
chr10:104852955	p.R367Q,NT5C2	3
chr10:104859732	p.R8Q,NT5C2	2
chr10:104851364	p.R195Q,NT5C2	2
chr10:104934693	p.E390K,NT5C2	2
chr10:104866349	p.T104T,NT5C2	1
chr10:104849467	p.K361N,NT5C2	1
chr10:104850727	p.T97N,NT5C2	1
chr10:104858711	p.E550K,NT5C2	1
chr10:104866423	p.K342N,NT5C2	1
chr10:104849492	p.L72L,NT5C2	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 NT5C2 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 NT5C2

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


ATL2,B3GNT5,CCDC82,CCNJ,CREB3L2,EML4,AMER1, FMNL2,JRKL,NT5C2,PADI2,PCGF6,PPRC1,SFT2D2, SMNDC1,STK38,TAF5,TTLL4,USP6NL,XPNPEP1,YEATS2	ANK3,KANSL2,TRMT13,DYRK1A,FAM160A1,LOC100128640,MTRF1, NAA25,NT5C2,PDE4B,PDE7A,PM20D2,PSTPIP2,RTF1, THAP9,TIAM2,TPP2,USP28,ZBTB43,ZC3H8,ZKSCAN5

ATAD1,BTRC,R3HCC1L,C10orf76,CPEB3,EXOC6,HERC4, LIPH,MARCH5,MGEA5,MXI1,MYOF,NT5C2,PLCE1, SEMA4G,SHOC2,SLC17A5,SLK,TBC1D12,TCF7L2,TM9SF3	ABHD3,ACER3,ACTR2,AHCYL2,B4GALT1,CEACAM1,DHRS9, FAM126B,FEM1C,GPD2,ITCH,MAPRE3,MIER3,NT5C2, RBM47,RNF6,SLC26A3,TMEM65,TMPRSS2,XIAP,YWHAB

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 NT5C2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB00171	5'-nucleotidase, cytosolic II	approved; nutraceutical	Adenosine triphosphate
DB00811	5'-nucleotidase, cytosolic II	approved	Ribavirin
DB00173	5'-nucleotidase, cytosolic II	approved; nutraceutical	Adenine
DB00515	5'-nucleotidase, cytosolic II	approved	Cisplatin
DB00441	5'-nucleotidase, cytosolic II	approved	Gemcitabine
DB00987	5'-nucleotidase, cytosolic II	approved; investigational	Cytarabine
DB00640	5'-nucleotidase, cytosolic II	approved; investigational	Adenosine

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Cross referenced IDs for NT5C2

* 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