Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 GPCPD1
Basic gene info.Gene symbolGPCPD1
Gene nameglycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)
SynonymsGDE5|GDPD6|PREI4
CytomapUCSC genome browser: 20p12.3
Genomic locationchr20 :5525079-5591672
Type of geneprotein-coding
RefGenesNM_019593.3,
Ensembl idENSG00000125772
Descriptionglycerophosphocholine phosphodiesterase GPCPD1glycerophosphodiester phosphodiesterase 5preimplantation protein 4putative glycerophosphocholine phosphodiesterase GPCPD1putative glycerophosphodiester phosphodiesterase 5
Modification date20141207
dbXrefs MIM : 614124
HGNC : HGNC
Ensembl : ENSG00000125772
HPRD : 10025
Vega : OTTHUMG00000031806
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPCPD1
BioGPS: 56261
Gene Expression Atlas: ENSG00000125772
The Human Protein Atlas: ENSG00000125772
PathwayNCI Pathway Interaction Database: GPCPD1
KEGG: GPCPD1
REACTOME: GPCPD1
ConsensusPathDB
Pathway Commons: GPCPD1
MetabolismMetaCyc: GPCPD1
HUMANCyc: GPCPD1
RegulationEnsembl's Regulation: ENSG00000125772
miRBase: chr20 :5,525,079-5,591,672
TargetScan: NM_019593
cisRED: ENSG00000125772
ContextiHOP: GPCPD1
cancer metabolism search in PubMed: GPCPD1
UCL Cancer Institute: GPCPD1
Assigned class in ccmGDBC

Top
Phenotypic Information for GPCPD1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GPCPD1
Familial Cancer Database: GPCPD1
* 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
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GPCPD1
MedGen: GPCPD1 (Human Medical Genetics with Condition)
ClinVar: GPCPD1
PhenotypeMGI: GPCPD1 (International Mouse Phenotyping Consortium)
PhenomicDB: GPCPD1

Mutations for GPCPD1
* 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
pancreasGPCPD1chr2055282065528226GPCPD1chr2055401865540206
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 GPCPD1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE763222FSTL111503120113901120114050GPCPD11381892055428465542897
AW813838SYTL4106497X9997168999972080GPCPD14896742055686885568875
AW889516GPCPD1132242055428465543057FSTL12123943120113901120114083

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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1     1   1      
GAIN (# sample)1     1   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)

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=41)
Stat. for Synonymous SNVs
(# total SNVs=15)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr20:5574004-5574004p.R67H3
chr20:5559069-5559069p.T221M2
chr20:5556455-5556455p.?2
chr20:5564940-5564940p.Q112Q2
chr20:5539438-5539438p.P520P2
chr20:5559154-5559154p.D193Y2
chr20:5564963-5564963p.E105K2
chr20:5566845-5566845p.P101L2
chr20:5545686-5545686p.Q436E2
chr20:5566888-5566888p.V87F1

Top
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
# sample1117  1 2  811  56 8
# mutation1117  1 2  811  56 9
nonsynonymous SNV1 15  1 2  7 1  54 7
synonymous SNV 1 2       11    2 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])

Top
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
chr20:5559069p.R67H2
chr20:5559154p.T221M2
chr20:5574004p.D193Y2
chr20:5528362p.S652F1
chr20:5566885p.C256Y1
chr20:5554591p.V87F1
chr20:5528371p.P650T1
chr20:5566888p.D246N1
chr20:5554612p.G81C1
chr20:5559074p.P643H1

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 GPCPD1 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 GPCPD1

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))
Top
check002.gifCNV 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
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

BCAP29,C20orf196,CASP10,CASP8,DNAJB3,ELL2,FRMD4B,
FZD4,GPCPD1,ITGB6,KAT2B,LPAR6,LTF,MMP21,
NUMB,PRKAA1,RALGAPA2,SLC28A3,SPTLC3,TC2N,UGT1A1
ATL2,CCDC14,CDK6,CHST9,DSC2,EML4,EPHA7,
GPCPD1,ITPR2,LOC284578,LOC286467,MBTD1,PMS1,SLCO1A2,
SNHG4,STX16,TAF4B,TET2,ZNF121,ZNF518A,ZNF562

C20orf196,C20orf96,CDS2,CRLS1,CSNK2A1,CSRP2BP,ESF1,
FAM156A,FERMT1,GPCPD1,KANK1,MAVS,MCM8,PLCB4,
SNRPB2,SPIN3,TASP1,TRMT6,ZCCHC3,ZNF133,ZNF343
ALOXE3,B4GALT6,VCPKMT,CACNB2,CDK17,E2F6,GJA1,
GPCPD1,HNRNPDL,MAP3K14,NAA16,PHF20L1,PRR3,REV1,
RPS6KB1,RUFY2,SENP2,U2SURP,UPF3A,ZMYM5,ZBTB18
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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for GPCPD1


There's no related Drug.
Top
Cross referenced IDs for GPCPD1
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas