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 PCYT1A
Basic gene info.Gene symbolPCYT1A
Gene namephosphate cytidylyltransferase 1, choline, alpha
SynonymsCCTA|CT|CTA|CTPCT|PCYT1|SMDCRD
CytomapUCSC genome browser: 3q29
Genomic locationchr3 :195965252-196014584
Type of geneprotein-coding
RefGenesNM_005017.2,
Ensembl idENSG00000161217
DescriptionCCT ACCT-alphaCT ACTP:phosphocholine cytidylyltransferase Acholine-phosphate cytidylyltransferase Aphosphorylcholine transferase A
Modification date20141207
dbXrefs MIM : 123695
HGNC : HGNC
HPRD : 00438
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PCYT1A
BioGPS: 5130
Gene Expression Atlas: ENSG00000161217
The Human Protein Atlas: ENSG00000161217
PathwayNCI Pathway Interaction Database: PCYT1A
KEGG: PCYT1A
REACTOME: PCYT1A
ConsensusPathDB
Pathway Commons: PCYT1A
MetabolismMetaCyc: PCYT1A
HUMANCyc: PCYT1A
RegulationEnsembl's Regulation: ENSG00000161217
miRBase: chr3 :195,965,252-196,014,584
TargetScan: NM_005017
cisRED: ENSG00000161217
ContextiHOP: PCYT1A
cancer metabolism search in PubMed: PCYT1A
UCL Cancer Institute: PCYT1A
Assigned class in ccmGDBC

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Phenotypic Information for PCYT1A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PCYT1A
Familial Cancer Database: PCYT1A
* 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_GLYCEROPHOSPHOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PCYT1A
MedGen: PCYT1A (Human Medical Genetics with Condition)
ClinVar: PCYT1A
PhenotypeMGI: PCYT1A (International Mouse Phenotyping Consortium)
PhenomicDB: PCYT1A

Mutations for PCYT1A
* 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
* 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastPCYT1Achr3195995359195995359PCYT1Achr3195995922195995922
ovaryPCYT1Achr3195982987195983007IGF2BP2chr3185528950185528970
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 PCYT1A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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  1     2 1      
GAIN (# sample)  1     2 1      
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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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=21)
Stat. for Synonymous SNVs
(# total SNVs=18)
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
chr3:195975094-195975094p.T106T3
chr3:195968877-195968877p.A217V2
chr3:195997349-195997349p.A18A2
chr3:195968927-195968927p.I200I2
chr3:195968873-195968873p.R218S1
chr3:195997312-195997312p.P31S1
chr3:195974240-195974240p.R162W1
chr3:195975116-195975116p.A99V1
chr3:195965646-195965646p.S339S1
chr3:195997337-195997337p.N22N1

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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
# sample121122 2  1 311  57 5
# mutation121122 2  1 311  58 5
nonsynonymous SNV12151 1    2    38 2
synonymous SNV   71 1  1 111  2  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
chr3:195997349p.A18A2
chr3:195968927p.I200I2
chr3:195969477p.G306V1
chr3:195975092p.R132S1
chr3:195997296p.P31S1
chr3:195965715p.L242F1
chr3:195974240p.N128N1
chr3:195975103p.N22N1
chr3:195997312p.R218S1
chr3:195965746p.L117L1

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 PCYT1A 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 PCYT1A

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

ACAP2,ATP13A3,DCUN1D1,DLG1,EIF4G1,FBXO45,FYTTD1,
KIAA0226,LRCH3,LSG1,MAP3K2,MFN1,OPA1,PAK2,
PCYT1A,PPP1R2P3,PSMD2,RNF168,SENP5,SLC33A1,UBXN7
ABCC9,ANKRD40,NATD1,DIP2C,RMDN1,FOXN3,HSDL2,
IGF2R,LIMS1,NEK9,NPLOC4,PCYT1A,PTPN11,RNF150,
SEC23A,SETD7,SGCB,SH3GLB1,TTC7B,YPEL2,YWHAG

ACAP2,GPATCH11,CCNT1,CFLAR,DCUN1D1,DDI2,DNAJC13,
LMBRD2,LUZP1,MOB1A,OSBPL11,PCYT1A,PLEKHB2,PPARGC1B,
PSMD2,PTPLB,RASA2,RNF168,SAMD8,SLCO2B1,UBXN7
ADIPOR2,EIF2AK2,ERBB2IP,G3BP2,HKDC1,KIF2A,MAP3K2,
MAPK6,PATL1,PCYT1A,PICALM,PSMD11,PSMD1,RRAGC,
SEC24A,SLC31A1,SPAG9,UBQLN1,UGCG,VTI1A,XRN1
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 PCYT1A
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
DB00122phosphate cytidylyltransferase 1, choline, alphaapproved; nutraceuticalCholine
DB00709phosphate cytidylyltransferase 1, choline, alphaapproved; investigationalLamivudine
DB00171phosphate cytidylyltransferase 1, choline, alphaapproved; nutraceuticalAdenosine triphosphate


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Cross referenced IDs for PCYT1A
* 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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