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 PCYT2
Basic gene info.Gene symbolPCYT2
Gene namephosphate cytidylyltransferase 2, ethanolamine
SynonymsET
CytomapUCSC genome browser: 17q25.3
Genomic locationchr17 :79860776-79869340
Type of geneprotein-coding
RefGenesNM_001184917.2,
NM_001256433.2,NM_001256434.2,NM_001256435.2,NM_001282203.1,
NM_001282204.1,NM_002861.4,
Ensembl idENSG00000185813
DescriptionCTP:phosphoethanolamine cytidylyltransferaseethanolamine-phosphate cytidylyltransferasephosphorylethanolamine transferase
Modification date20141207
dbXrefs MIM : 602679
HGNC : HGNC
HPRD : 04059
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PCYT2
BioGPS: 5833
Gene Expression Atlas: ENSG00000185813
The Human Protein Atlas: ENSG00000185813
PathwayNCI Pathway Interaction Database: PCYT2
KEGG: PCYT2
REACTOME: PCYT2
ConsensusPathDB
Pathway Commons: PCYT2
MetabolismMetaCyc: PCYT2
HUMANCyc: PCYT2
RegulationEnsembl's Regulation: ENSG00000185813
miRBase: chr17 :79,860,776-79,869,340
TargetScan: NM_001184917
cisRED: ENSG00000185813
ContextiHOP: PCYT2
cancer metabolism search in PubMed: PCYT2
UCL Cancer Institute: PCYT2
Assigned class in ccmGDBC

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Phenotypic Information for PCYT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PCYT2
Familial Cancer Database: PCYT2
* 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: PCYT2
MedGen: PCYT2 (Human Medical Genetics with Condition)
ClinVar: PCYT2
PhenotypeMGI: PCYT2 (International Mouse Phenotyping Consortium)
PhenomicDB: PCYT2

Mutations for PCYT2
* 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
ovaryPCYT2chr177986237779862397chr204473343444733454
ovaryPCYT2chr177986306379863083MED1chr173758622937586249
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 PCYT2 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
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=17)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr17:79867402-79867402p.V56M3
chr17:79864762-79864762p.R184W2
chr17:79866482-79866482p.R123R2
chr17:79866776-79866776p.N106H1
chr17:79863320-79863320p.D303N1
chr17:79864701-79864701p.A204V1
chr17:79866785-79866785p.D103H1
chr17:79863585-79863585p.A288A1
chr17:79864720-79864720p.Q198E1
chr17:79862724-79862724p.R385R1

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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
# sample21 11 2 2  2    45 3
# mutation21 11 2 2  2    46 3
nonsynonymous SNV11 11 1    1    25 1
synonymous SNV1     1 2  1    21 2
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
chr17:79867402p.V56M,PCYT22
chr17:79864762p.N306K,PCYT21
chr17:79867409p.I83I,PCYT21
chr17:79864773p.A304A,PCYT21
chr17:79867430p.G67G,PCYT21
chr17:79862799p.F277F,PCYT21
chr17:79865452p.T58I,PCYT21
chr17:79867459p.A223S,PCYT21
chr17:79862805p.F171F,PCYT21
chr17:79865653p.I53I,PCYT21

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 PCYT2 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 PCYT2

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

ANAPC11,ARHGDIA,ARL16,ASPSCR1,C17orf89,OXLD1,CCDC137,
DCXR,DUS1L,FAM195B,GPS1,HGS,LRRC45,MRPL12,
MRPL38,PCYT2,RAC3,RFNG,SIRT7,SLC25A10,STRA13
ALDH1L1,ASS1,C17orf53,IZUMO4,C20orf27,APMAP,ECHDC3,
FASN,GCDH,GLUL,GLYCTK,MPST,NDRG4,PC,
PCYT2,PMM1,PXMP2,RASL10B,SHMT1,SLC25A1,TMEM120A

ATP5D,UQCC3,COX8A,DCXR,DUS1L,GPS1,LRRC45,
MRPL12,MRPL38,NAPRT,NDUFS8,NT5C,PCYT2,PYCR1,
RFNG,RNF126,SIRT7,SLC25A10,SLC25A39,SURF2,TSEN54
AGMAT,AIMP2,AKR7A3,DNPH1,CENPV,CISD3,COQ4,
FAM195A,FAM35A,FAM35BP,HADH,IMP3,MTCH2,NDUFC2,
OXNAD1,PCYT2,PRR5,SHMT1,SLC25A10,SUCLG1,TRAF4
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 PCYT2
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
DB00709phosphate cytidylyltransferase 2, ethanolamineapproved; investigationalLamivudine


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Cross referenced IDs for PCYT2
* 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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