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 GMPR2

Basic gene info.	Gene symbol	GMPR2
	Gene name	guanosine monophosphate reductase 2
	Synonyms	-
	Cytomap	UCSC genome browser: 14q12
	Genomic location	chr14 :24701647-24708447
	Type of gene	protein-coding
	RefGenes	NM_001002000.2, NM_001002001.2,NM_001002002.2,NM_001283021.1,NM_001283022.1, NM_001283023.1,NM_016576.4,NR_104265.1,
	Ensembl id	ENSG00000100938
	Description	GMP reductase 2guanosine 5'-monophosphate oxidoreductase 2guanosine monophosphate reductase isolog
	Modification date	20141207
dbXrefs	MIM : 610781
	HGNC : HGNC
	Ensembl : ENSG00000100938
	HPRD : 13590
	Vega : OTTHUMG00000171912
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GMPR2
	BioGPS: 51292
	Gene Expression Atlas: ENSG00000100938
	The Human Protein Atlas: ENSG00000100938
Pathway	NCI Pathway Interaction Database: GMPR2
	KEGG: GMPR2
	REACTOME: GMPR2
	ConsensusPathDB
	Pathway Commons: GMPR2
Metabolism	MetaCyc: GMPR2
	HUMANCyc: GMPR2
Regulation	Ensembl's Regulation: ENSG00000100938
	miRBase: chr14 :24,701,647-24,708,447
	TargetScan: NM_001002000
	cisRED: ENSG00000100938
Context	iHOP: GMPR2
	cancer metabolism search in PubMed: GMPR2
	UCL Cancer Institute: GMPR2
Assigned class in ccmGDB	C

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Phenotypic Information for GMPR2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GMPR2
	Familial Cancer Database: GMPR2

* 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 REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PURINE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: GMPR2
	MedGen: GMPR2 (Human Medical Genetics with Condition)
	ClinVar: GMPR2
Phenotype	MGI: GMPR2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GMPR2

Mutations for GMPR2

* 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 GMPR2 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
AK075025	GMPR2	1	1165	14	24701666	24707667	STOML2	1161	2064	9	35099893	35101490
BF916399	JUN	1	123	1	59247923	59248045	GMPR2	116	288	14	24708184	24708356

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=13)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=1)	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
chr14:24707977-24707977	p.A347V	2
chr14:24702539-24702539	p.R27Q	2
chr14:24706339-24706339	p.I176M	2
chr14:24702518-24702518	p.K20R	1
chr14:24706347-24706347	p.G179E	1
chr14:24707610-24707610	p.R286*	1
chr14:24702528-24702528	p.T23T	1
chr14:24706350-24706350	p.I180S	1
chr14:24707797-24707797	p.A287V	1
chr14:24706359-24706359	p.?	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		5			1					2		2			3	2		5
# mutation		1		4			1					2		2			3	2		6
nonsynonymous SNV		1		2			1							2			2	1		3
synonymous SNV				2								2					1	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
chr14:24702528	p.T41T,GMPR2	2
chr14:24702445	p.G260R,GMPR2	1
chr14:24706750	p.L263L,GMPR2	1
chr14:24702464	p.F361V,GMPR2	1
chr14:24706767	p.P14S,GMPR2	1
chr14:24707478	p.A366V,GMPR2	1
chr14:24702538	p.P20L,GMPR2	1
chr14:24707487	p.G369E,GMPR2	1
chr14:24702774	p.V374L,GMPR2	1
chr14:24707781	p.R45R,GMPR2	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 GMPR2 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 GMPR2

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


ACOT4,AP1G2,DHRS4-AS1,DCAF11,EAPP,GMPR2,HOMEZ, KHNYN,KLHDC2,LRP10,MDP1,NEDD8,OXA1L,PIGH, PSME1,RNF31,THTPA,TINF2,TM9SF1,TOX4,TTC8	ARMCX6,C10orf35,C11orf52,C14orf93,DALRD3,DGCR2,DNAL4, ELMO3,FBL,GMPR2,ING4,MED29,MRFAP1L1,MRPL49, NR2C2AP,PRKCZ,RAB25,RPL3,SPINT2,STK16,TTLL1

ALKBH1,APEX1,DNAAF2,C14orf119,DTD2,C14orf166,CGRRF1, CHMP4A,CNIH1,DAD1,EAPP,GMPR2,HAUS4,ISCA2, KIAA0391,MDP1,NEDD8,RPS29,SNX6,TMEM55B,ZNF410	BLOC1S1,TEN1,LINC00324,RPP25L,CCNDBP1,CHMP5,DERA, EAPP,GABARAP,GMPR2,HINFP,HOXB7,MAT2B,OAZ1, LAMTOR2,SAT1,TMEM219,TMEM59,UBAC2,VPS28,ZNF706

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 GMPR2

There's no related Drug.

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Cross referenced IDs for GMPR2

* 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