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 GMPS

Basic gene info.	Gene symbol	GMPS
	Gene name	guanine monphosphate synthase
	Synonyms	-
	Cytomap	UCSC genome browser: 3q24
	Genomic location	chr3 :155588324-155655520
	Type of gene	protein-coding
	RefGenes	NM_003875.2,
	Ensembl id	ENSG00000163655
	Description	GMP synthaseGMP synthase [glutamine-hydrolyzing]GMP synthetaseMLL/GMPS fusion proteinglutamine amidotransferaseguanine monphosphate synthetaseguanosine 5'-monophosphate synthase
	Modification date	20141207
dbXrefs	MIM : 600358
	HGNC : HGNC
	Ensembl : ENSG00000163655
	HPRD : 10927
	Vega : OTTHUMG00000158551
Protein	UniProt: P49915 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GMPS
	BioGPS: 8833
	Gene Expression Atlas: ENSG00000163655
	The Human Protein Atlas: ENSG00000163655
Pathway	NCI Pathway Interaction Database: GMPS
	KEGG: GMPS
	REACTOME: GMPS
	ConsensusPathDB
	Pathway Commons: GMPS
Metabolism	MetaCyc: GMPS
	HUMANCyc: GMPS
Regulation	Ensembl's Regulation: ENSG00000163655
	miRBase: chr3 :155,588,324-155,655,520
	TargetScan: NM_003875
	cisRED: ENSG00000163655
Context	iHOP: GMPS
	cancer metabolism search in PubMed: GMPS
	UCL Cancer Institute: GMPS
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: GMPS
	Familial Cancer Database: GMPS

* 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_DRUG_METABOLISM_OTHER_ENZYMES REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PURINE_METABOLISM

Others
OMIM	600358; gene.
Orphanet
Disease	KEGG Disease: GMPS
	MedGen: GMPS (Human Medical Genetics with Condition)
	ClinVar: GMPS
Phenotype	MGI: GMPS (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GMPS

Mutations for GMPS

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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	GMPS	chr3	155642643	155642663	GMPS	chr3	155642549	155642569
ovary	GMPS	chr3	155649791	155649811	GMPS	chr3	155650012	155650032

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 GMPS 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
AF297747	MLL	2	426	11	118352703	118355690	GMPS	425	1586	3	155611305	155633956
AF297748	MLL	1	171	11	118353172	118355029	GMPS	170	353	3	155611305	155611488
AF297746	MLL	2	312	11	118352703	118355029	GMPS	311	658	3	155611305	155621700
AF297749	MLL	1	285	11	118353172	118355690	GMPS	284	467	3	155611305	155611488
AU132130	CCDC141	1	512	2	179912011	179916447	GMPS	511	694	3	155611305	155611489

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=68)	Stat. for Synonymous SNVs (# total SNVs=12)

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
chr3:155628985-155628985	p.V268A	3
chr3:155652794-155652794	p.R589H	3
chr3:155628496-155628496	p.S181F	3
chr3:155621691-155621691	p.S122G	2
chr3:155639983-155639983	p.G442G	2
chr3:155654194-155654194	p.L625L	2
chr3:155654195-155654195	p.Q626*	2
chr3:155652730-155652730	p.V568I	2
chr3:155652736-155652736	p.E570*	2
chr3:155655429-155655429	p.R677Q	2

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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=4

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	3	2	1	16			3			1		10	1	2			5	4	1	10
# mutation	3	2	1	15			3			1		11	1	2			6	4	1	12
nonsynonymous SNV	2	2	1	13			3			1		9		1			6	3	1	11
synonymous SNV	1			2								2	1	1				1		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
chr3:155652794	p.V268A	3
chr3:155628985	p.R589H	3
chr3:155655458	p.P687T	2
chr3:155615742	p.Q264R	1
chr3:155639983	p.I398I	1
chr3:155628609	p.P612P	1
chr3:155652728	p.V50M	1
chr3:155632262	p.V268M	1
chr3:155615754	p.G442D	1
chr3:155640006	p.R622L	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 GMPS 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 GMPS

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


BUB1,CCNB2,DLGAP5,EXO1,GMPS,KIF20A,KIF23, KIF4A,KPNA4,MCM6,MELK,MSH2,MSH6,NCAPG, PLCH1,RFC4,SMC4,STIL,SUV39H2,TPX2,TTK	CCDC138,DSC2,FAM60A,GMPS,HDAC2,LARS,LRRC8D, MSH2,MSH6,PAICS,PPAT,SEC23B,SET,SLC25A13, SRP72,SRPK1,STIL,TDP1,TEX10,TMEM97,ZNF146

ACTL6A,CMSS1,CHEK1,ECT2,FBXO45,GMPS,KIAA1524, MCM2,MRPL3,NAA50,NCAPH,POLQ,PRIM2,RFC4, RSRC1,RUVBL1,SMC4,TOPBP1,TRA2B,TTK,UMPS	CCT3,CCT6A,CHEK1,CSE1L,FAM98A,GMPS,HSPD1, IARS,IPO11,MCM6,NAA15,NOL10,PA2G4,PA2G4P4, PAICS,RUVBL1,SERBP1,SET,STIP1,USP1,ZW10

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 GMPS

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL5721; -.
Organism-specific databases	PharmGKB	PA28763; -.
Organism-specific databases	CTD	8833; -.

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
DB00142	guanine monphosphate synthase	approved; nutraceutical	L-Glutamic Acid
DB02212	guanine monphosphate synthase	experimental	Pyrophosphate 2-
DB04272	guanine monphosphate synthase	experimental	Citric Acid
DB00130	guanine monphosphate synthase	approved; nutraceutical; investigational	L-Glutamine

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Cross referenced IDs for GMPS

* 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