Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 CTPS2
Basic gene info.Gene symbolCTPS2
Gene nameCTP synthase 2
Synonyms-
CytomapUCSC genome browser: Xp22
Genomic locationchrX :16606121-16731059
Type of geneprotein-coding
RefGenesNM_001144002.1,
NM_019857.4,NM_175859.2,
Ensembl idENSG00000047230
DescriptionCTP synthase IICTP synthetase type 2UTP-ammonia ligase 2cytidine 5'-triphosphate synthetase 2
Modification date20141207
dbXrefs MIM : 300380
HGNC : HGNC
Ensembl : ENSG00000047230
HPRD : 02305
Vega : OTTHUMG00000021193
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CTPS2
BioGPS: 56474
Gene Expression Atlas: ENSG00000047230
The Human Protein Atlas: ENSG00000047230
PathwayNCI Pathway Interaction Database: CTPS2
KEGG: CTPS2
REACTOME: CTPS2
ConsensusPathDB
Pathway Commons: CTPS2
MetabolismMetaCyc: CTPS2
HUMANCyc: CTPS2
RegulationEnsembl's Regulation: ENSG00000047230
miRBase: chrX :16,606,121-16,731,059
TargetScan: NM_001144002
cisRED: ENSG00000047230
ContextiHOP: CTPS2
cancer metabolism search in PubMed: CTPS2
UCL Cancer Institute: CTPS2
Assigned class in ccmGDBC

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Phenotypic Information for CTPS2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CTPS2
Familial Cancer Database: CTPS2
* 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_PYRIMIDINE_METABOLISM
REACTOME_METABOLISM_OF_NUCLEOTIDES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CTPS2
MedGen: CTPS2 (Human Medical Genetics with Condition)
ClinVar: CTPS2
PhenotypeMGI: CTPS2 (International Mouse Phenotyping Consortium)
PhenomicDB: CTPS2

Mutations for CTPS2
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CTPS2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF839137CTPS2172304X1667256116672693SEC31A29850548380361883803824
BE826026ERCC12324194597798145978305CTPS2321389X1668485516684923
CV403184CTPS26152X1667380216673950CTPS2153372X1665986016660078

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
There's no copy number variation information in COSMIC data for this gene.

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=28)
Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr23:16627757-16627757p.P533L2
chr23:16720909-16720909p.I39I2
chr23:16716413-16716413p.Q128H2
chr23:16717110-16717110p.G91G1
chr23:16685651-16685651p.A428T1
chr23:16696555-16696555p.L342V1
chr23:16720890-16720890p.D46Y1
chr23:16711512-16711512p.H179H1
chr23:16685675-16685675p.D420N1
chr23:16717111-16717111p.G91V1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 3  1  1 624  52110
# mutation12 3  1  1 724  62212
nonsynonymous SNV 1 3       611  3216
synonymous SNV11    1  1 113  3 16
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
chrX:16720909p.I39I,CTPS22
chrX:16716377p.P140P,CTPS22
chrX:16696534p.P273L,CTPS21
chrX:16711541p.R454I,CTPS21
chrX:16657302p.V263L,CTPS21
chrX:16696535p.S29L,CTPS21
chrX:16720940p.M448T,CTPS21
chrX:16657320p.V241V,CTPS21
chrX:16696555p.S12S,CTPS21
chrX:16716452p.L432V,CTPS21

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 CTPS2 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 CTPS2

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

CTPS2,EIF1AX,EIF2S3,GRPR,GSPT1,HDHD1,HN1L,
MBTPS2,MED14,POLA1,PTGES3,RBBP7,REPS2,S100G,
SEPHS2,SLC17A4,SYAP1,TCEANC,TRAPPC2,TXLNG,USP9X
C2orf15,CDH1,CTPS2,DCLRE1A,ERBB3,ESRP1,KDM5B,
LRBA,MARVELD2,OCLN,RBBP4,SLC39A9,SPATS2,SPEF2,
STRBP,TEX9,TTC30B,TTC8,ZNF544,ZNF552,ZNF627

ARSE,ASB9,CTPS2,CXorf23,EIF2S3,FUNDC1,GEMIN8,
GJB1,MAGED2,MBTPS2,OFD1,JADE3,POLA1,RBBP7,
RPS6KA3,SCML1,SHROOM4,SYAP1,TAB3,ZDHHC9,KRBOX4
ALDH5A1,ALG9,CTPS2,EIF2AK4,KDM1A,LRP11,MBTPS1,
NONO,PABPC1,PAIP2B,PARP16,PLA2G12A,PLEKHA5,RBL2,
ST18,SUDS3,TBCK,TTC37,TTLL2,TXNDC16,ZNF146
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 CTPS2


There's no related Drug.
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Cross referenced IDs for CTPS2
* 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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