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 CPS1
Basic gene info.Gene symbolCPS1
Gene namecarbamoyl-phosphate synthase 1, mitochondrial
SynonymsCPSASE1|PHN
CytomapUCSC genome browser: 2q35
Genomic locationchr2 :211342405-211543831
Type of geneprotein-coding
RefGenesNM_001122633.2,
NM_001122634.2,NM_001875.4,
Ensembl idENSG00000021826
Descriptioncarbamoyl-phosphate synthase [ammonia], mitochondrialcarbamoylphosphate synthetase I
Modification date20141211
dbXrefs MIM : 608307
HGNC : HGNC
Ensembl : ENSG00000021826
HPRD : 01995
Vega : OTTHUMG00000132994
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CPS1
BioGPS: 1373
Gene Expression Atlas: ENSG00000021826
The Human Protein Atlas: ENSG00000021826
PathwayNCI Pathway Interaction Database: CPS1
KEGG: CPS1
REACTOME: CPS1
ConsensusPathDB
Pathway Commons: CPS1
MetabolismMetaCyc: CPS1
HUMANCyc: CPS1
RegulationEnsembl's Regulation: ENSG00000021826
miRBase: chr2 :211,342,405-211,543,831
TargetScan: NM_001122633
cisRED: ENSG00000021826
ContextiHOP: CPS1
cancer metabolism search in PubMed: CPS1
UCL Cancer Institute: CPS1
Assigned class in ccmGDBC

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Phenotypic Information for CPS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM
KEGG_ARGININE_AND_PROLINE_METABOLISM
KEGG_NITROGEN_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CPS1
MedGen: CPS1 (Human Medical Genetics with Condition)
ClinVar: CPS1
PhenotypeMGI: CPS1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryCPS1chr2211349759211349779CPS1chr2211345995211346015
ovaryCPS1chr2211432074211432094chr2212207968212207988
ovaryCPS1chr2211513531211513551CPS1chr2211513876211513896
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CPS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AV694689CPS12842211421361211421447PRDX37958310120927794120931984
BX102832CPS115112211523219211523729IFNGR14995806137518622137518703

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample             11  
GAIN (# sample)              1  
LOSS (# sample)             1   
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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check002.gifSNV 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

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check002.gifSomatic 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)

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr2:211540487-211540487p.N1399N5
chr2:211521298-211521298p.S1203L4
chr2:211441114-211441114p.L94P4
chr2:211455590-211455590p.A303S3
chr2:211456679-211456679p.D358N3
chr2:211459300-211459300p.P411P3
chr2:211512710-211512710p.R1089C3
chr2:211457685-211457685p.?2
chr2:211460236-211460236p.S430L2
chr2:211518789-211518789p.R1174Q2

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample671345 13 11  51248132221 13
# mutation771325 13 11  62308132623 22
nonsynonymous SNV571275 11 10  452741 1919 19
synonymous SNV2  5  2 1  1734 374 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr2:211441114p.L94P,CPS14
chr2:211540487p.N948N,CPS13
chr2:211464127p.L453V,CPS12
chr2:211456679p.S752P,CPS12
chr2:211459300p.M96V,CPS12
chr2:211502448p.P13Q,CPS12
chr2:211441119p.A97V,CPS12
chr2:211507249p.R238C,CPS12
chr2:211471538p.T398K,CPS12
chr2:211476995p.R866W,CPS12

check002.gifOther 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

check002.gifCopy 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]

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Gene Expression for CPS1

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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 CPS1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00125carbamoyl-phosphate synthase 1, mitochondrialapproved; nutraceuticalL-Arginine
DB03904carbamoyl-phosphate synthase 1, mitochondrialexperimentalUrea


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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



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