Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 CPS1

Basic gene info.	Gene symbol	CPS1
	Gene name	carbamoyl-phosphate synthase 1, mitochondrial
	Synonyms	CPSASE1\|PHN
	Cytomap	UCSC genome browser: 2q35
	Genomic location	chr2 :211342405-211543831
	Type of gene	protein-coding
	RefGenes	NM_001122633.2, NM_001122634.2,NM_001875.4,
	Ensembl id	ENSG00000021826
	Description	carbamoyl-phosphate synthase [ammonia], mitochondrialcarbamoylphosphate synthetase I
	Modification date	20141211
dbXrefs	MIM : 608307
	HGNC : HGNC
	Ensembl : ENSG00000021826
	HPRD : 01995
	Vega : OTTHUMG00000132994
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CPS1
	BioGPS: 1373
	Gene Expression Atlas: ENSG00000021826
	The Human Protein Atlas: ENSG00000021826
Pathway	NCI Pathway Interaction Database: CPS1
	KEGG: CPS1
	REACTOME: CPS1
	ConsensusPathDB
	Pathway Commons: CPS1
Metabolism	MetaCyc: CPS1
	HUMANCyc: CPS1
Regulation	Ensembl's Regulation: ENSG00000021826
	miRBase: chr2 :211,342,405-211,543,831
	TargetScan: NM_001122633
	cisRED: ENSG00000021826
Context	iHOP: CPS1
	cancer metabolism search in PubMed: CPS1
	UCL Cancer Institute: CPS1
Assigned class in ccmGDB	C

Top

Phenotypic Information for CPS1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CPS1
	Familial Cancer Database: CPS1

* 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_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM KEGG_ARGININE_AND_PROLINE_METABOLISM KEGG_NITROGEN_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM
Orphanet
Disease	KEGG Disease: CPS1
	MedGen: CPS1 (Human Medical Genetics with Condition)
	ClinVar: CPS1
Phenotype	MGI: CPS1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CPS1

Mutations for CPS1

* 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

Top

- 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	CPS1	chr2	211349759	211349779	CPS1	chr2	211345995	211346015
ovary	CPS1	chr2	211432074	211432094		chr2	212207968	212207988
ovary	CPS1	chr2	211513531	211513551	CPS1	chr2	211513876	211513896

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 CPS1 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
AV694689	CPS1	2	84	2	211421361	211421447	PRDX3	79	583	10	120927794	120931984
BX102832	CPS1	1	511	2	211523219	211523729	IFNGR1	499	580	6	137518622	137518703

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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=8

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=237)	Stat. for Synonymous SNVs (# total SNVs=57)

Stat. for Deletions (# total SNVs=5)	Stat. for Insertions (# total SNVs=1)

Top

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
chr2:211540487-211540487	p.N1399N	5
chr2:211441114-211441114	p.L94P	4
chr2:211521298-211521298	p.S1203L	4
chr2:211455590-211455590	p.A303S	3
chr2:211456679-211456679	p.D358N	3
chr2:211459300-211459300	p.P411P	3
chr2:211512710-211512710	p.R1089C	3
chr2:211476995-211476995	p.T849K	2
chr2:211457661-211457661	p.P382Q	2
chr2:211532932-211532932	p.I1342S	2

Top

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	6	7	1	34	5		13		11			51	24	8	1	3	22	21		13
# mutation	7	7	1	32	5		13		11			62	30	8	1	3	26	23		22
nonsynonymous SNV	5	7	1	27	5		11		10			45	27	4	1		19	19		19
synonymous SNV	2			5			2		1			17	3	4		3	7	4		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])

Top

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
chr2:211441114	p.L94P,CPS1	4
chr2:211540487	p.N948N,CPS1	3
chr2:211441119	p.F824L,CPS1	2
chr2:211507249	p.D358N,CPS1	2
chr2:211471538	p.L453V,CPS1	2
chr2:211476995	p.S752P,CPS1	2
chr2:211441123	p.M96V,CPS1	2
chr2:211541795	p.P13Q,CPS1	2
chr2:211521297	p.A97V,CPS1	2
chr2:211541814	p.T398K,CPS1	2

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 CPS1 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]

Top

Gene Expression for CPS1

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


APCS,APOA2,APOA4,APOB,ARG1,CPS1,CRP, F11,F2,FABP1,FGF23,GC,GDF2,HP, LOC29034,MT1B,MT1F,MT1M,SERPINA7,SLC17A2,TM4SF5	AK3___AK4,BAG4,BTBD8,C11orf63,CPS1,KIAA1107,MID2, MSH3,PRICKLE2,PTEN,PTENP1,PTPLB,PTPRG,MIEF1, STAT5B,TFDP2,TTC3,TXLNG,UBE4A,ZHX1,ZNF391

A4GNT,ACY3,ANXA10,BCAR4,BTBD16,CCER1,CLTC, COX8C,CPS1,CYB561,CYP2E1,GABRP,GATA4,GATM, KY,LIPC,LOC100128239,PDZK1,RPS6KB1,SERPINA4,SLC16A2	APOA1,APOA4,APOB,APOC3,C17orf78,CPO,CPS1, CRISP1,CUBN,ENPEP,FAM99A,FAM99B,GSTA5,KCNJ13, LCE3E,LOC388428,MOS,ONECUT3,OR10H1,OR10H5,OR4N5, PWAR4___F2RL3___PAWR,SPANXN3,TMPR

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for CPS1

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
DB00125	carbamoyl-phosphate synthase 1, mitochondrial	approved; nutraceutical	L-Arginine
DB03904	carbamoyl-phosphate synthase 1, mitochondrial	experimental	Urea

Top

Cross referenced IDs for CPS1

* 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