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 OPLAH
Basic gene info.Gene symbolOPLAH
Gene name5-oxoprolinase (ATP-hydrolysing)
Synonyms5-Opase|OPLA|OPLAHD
CytomapUCSC genome browser: 8q24.3
Genomic locationchr8 :145106166-145115584
Type of geneprotein-coding
RefGenesNM_017570.4,
Ensembl idENSG00000261479
Description5-oxo-L-prolinase5-oxoprolinasepyroglutamase
Modification date20141211
dbXrefs MIM : 614243
HGNC : HGNC
Ensembl : ENSG00000178814
HPRD : 14880
Vega : OTTHUMG00000165435
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_OPLAH
BioGPS: 26873
Gene Expression Atlas: ENSG00000261479
The Human Protein Atlas: ENSG00000261479
PathwayNCI Pathway Interaction Database: OPLAH
KEGG: OPLAH
REACTOME: OPLAH
ConsensusPathDB
Pathway Commons: OPLAH
MetabolismMetaCyc: OPLAH
HUMANCyc: OPLAH
RegulationEnsembl's Regulation: ENSG00000261479
miRBase: chr8 :145,106,166-145,115,584
TargetScan: NM_017570
cisRED: ENSG00000261479
ContextiHOP: OPLAH
cancer metabolism search in PubMed: OPLAH
UCL Cancer Institute: OPLAH
Assigned class in ccmGDBC

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

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

Mutations for OPLAH
* 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 OPLAH 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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=65)
Stat. for Synonymous SNVs
(# total SNVs=21)
Stat. for Deletions
(# total SNVs=5)
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
chr8:145109542-145109542p.H870fs*283
chr8:145114844-145114844p.R31Q2
chr8:145111332-145111332p.E647K2
chr8:145113014-145113014p.F329F2
chr8:145113912-145113912p.G145E2
chr8:145107490-145107490p.A1055A2
chr8:145114845-145114845p.R31W2
chr8:145113930-145113930p.R139H2
chr8:145111529-145111529p.F612F2
chr8:145112502-145112502p.R424H2

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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
# sample 6191 3    87   111015
# mutation 61131 3    87   151016
nonsynonymous SNV 3191 2    65   64 4
synonymous SNV 3 4  1    22   9612
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
chr8:145108219p.R424H2
chr8:145112765p.D922Y2
chr8:145112502p.R384C2
chr8:145106851p.N1079N1
chr8:145111556p.H856D1
chr8:145114840p.L562L1
chr8:145108212p.Y302C1
chr8:145112528p.A1074V1
chr8:145109753p.D831H1
chr8:145113227p.V559V1

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 OPLAH 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 OPLAH

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

ADCK5,ARHGAP39,HGH1,COMMD5,CPSF1,CYC1,FAM83H,
GPAA1,MROH1,HSF1,LRRC14,MAF1,OPLAH,PPP1R16A,
PUF60,PYCRL,SCRIB,SHARPIN,TIGD5,ZC3H3,ZNF707
ACY1,ATG2A,BAG6,BCKDHA,ECI1,DHODH,DNAJA3,
DNAJC11,ESRRA,INTS1,CLUH,LONP1,MYH14,OPLAH,
POLRMT,PPP1R16A,PRMT7,RNMTL1,RPTOR,TIMM44,WDR24

ADCK5,ARHGAP39,HGH1,CPSF1,CYHR1,DGAT1,EXOSC4,
FAM83H,FBXL6,MROH1,KIFC2,LRRC14,MFSD3,OPLAH,
PARP10,PPP1R16A,SCRIB,SHARPIN,SLC29A2,TIGD5,TOP1MT
ABR,ADCY6,CC2D1A,CDK16,CTDP1,DGKQ,EDC4,
EPHA10,FUK,HDAC6,CAMSAP3,MAST3,OPLAH,PCNXL3,
PLA2G6,POLRMT,RABEP2,SCAP,STK11,TRPM4,ZDHHC7
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 OPLAH
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
DB001425-oxoprolinase (ATP-hydrolysing)approved; nutraceuticalL-Glutamic Acid


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Cross referenced IDs for OPLAH
* 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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