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 CPOX
Basic gene info.Gene symbolCPOX
Gene namecoproporphyrinogen oxidase
SynonymsCPO|CPX|HCP
CytomapUCSC genome browser: 3q12
Genomic locationchr3 :98298289-98312455
Type of geneprotein-coding
RefGenesNM_000097.5,
Ensembl idENSG00000080819
DescriptionCOXcoprogen oxidasecoproporphyrinogen-III oxidase, mitochondrialcoproporphyrinogenaseoxygen-dependent coproporphyrinogen-III oxidase, mitochondrial
Modification date20141219
dbXrefs MIM : 612732
HGNC : HGNC
Ensembl : ENSG00000080819
HPRD : 00417
Vega : OTTHUMG00000160016
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CPOX
BioGPS: 1371
Gene Expression Atlas: ENSG00000080819
The Human Protein Atlas: ENSG00000080819
PathwayNCI Pathway Interaction Database: CPOX
KEGG: CPOX
REACTOME: CPOX
ConsensusPathDB
Pathway Commons: CPOX
MetabolismMetaCyc: CPOX
HUMANCyc: CPOX
RegulationEnsembl's Regulation: ENSG00000080819
miRBase: chr3 :98,298,289-98,312,455
TargetScan: NM_000097
cisRED: ENSG00000080819
ContextiHOP: CPOX
cancer metabolism search in PubMed: CPOX
UCL Cancer Institute: CPOX
Assigned class in ccmGDBC

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

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

Mutations for CPOX
* 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 CPOX 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=32)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr3:98300354-98300354p.Y392D2
chr3:98312096-98312096p.L85V2
chr3:98312188-98312188p.A54D2
chr3:98309955-98309955p.E201K2
chr3:98307630-98307630p.V294F2
chr3:98311863-98311863p.Q162H1
chr3:98304461-98304461p.R332R1
chr3:98299542-98299542p.R450R1
chr3:98307696-98307696p.N272H1
chr3:98311879-98311879p.L157Q1

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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   5  1 11 531 24316
# mutation   5  1 11 531 26316
nonsynonymous SNV   3  1 1  421 24215
synonymous SNV   2     1 11   21 1
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
chr3:98304389p.E153V1
chr3:98307680p.R328H1
chr3:98299542p.A110A1
chr3:98312019p.R450R1
chr3:98304422p.D321V1
chr3:98309560p.P103H1
chr3:98299547p.P449T1
chr3:98312041p.F315L1
chr3:98304426p.L85V1
chr3:98309567p.R447S1

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 CPOX 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 CPOX

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

ATP2C1,B3GNT5,MSANTD3,CBFB,CLDND1,CPOX,DCBLD2,
EML4,GTPBP8,IQCB1,KIAA1524,LBR,NAA50,POLQ,
SKP2,SLC9A6,SMC6,TBC1D23,TOPBP1,YEATS2,ZDHHC23
AASDHPPT,ABCB10,KANSL1L,C5orf24,CPOX,DR1,FAM76B,
FMR1,GABPA,POLR2M___GCOM1,KLHL28,PAPD4,RCOR3,SCAI,
SMAD4,SPAST,STYX,TAF5,TIAL1,YY1,ZNF569

ABHD10,CDCA2,CLDND1,CPOX,DEPDC1,DTL,ECT2,
EXO1,LARP1B,MLN,NMD3,PBK,RAD21L1,RRM2,
RSRC1,SFXN1,SSR3,TIFA,TMEM233,UBA5,UGT8
ACVR1C,ALDH5A1,TMEM260,CDC40,CPOX,ERLIN2,FKTN,
FNBP1L,GCNT1,GLCE,IDH1,JRKL,KIAA1804,MBTD1,
MED23,NRIP1,RBBP5,SLC12A2,STAMBPL1,TBC1D8B,TRIM2
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 CPOX
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
DB03766coproporphyrinogen oxidaseexperimentalPropanoic Acid
DB03793coproporphyrinogen oxidaseexperimentalBenzoic Acid
DB00145coproporphyrinogen oxidaseapproved; nutraceuticalGlycine


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Cross referenced IDs for CPOX
* 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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