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 PPOX
Basic gene info.Gene symbolPPOX
Gene nameprotoporphyrinogen oxidase
SynonymsPPO|V290M|VP
CytomapUCSC genome browser: 1q22
Genomic locationchr1 :161136180-161141010
Type of geneprotein-coding
RefGenesNM_000309.3,
NM_001122764.1,
Ensembl idENSG00000143224
Description-
Modification date20141219
dbXrefs MIM : 600923
HGNC : HGNC
Ensembl : ENSG00000143224
HPRD : 02953
Vega : OTTHUMG00000034342
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PPOX
BioGPS: 5498
Gene Expression Atlas: ENSG00000143224
The Human Protein Atlas: ENSG00000143224
PathwayNCI Pathway Interaction Database: PPOX
KEGG: PPOX
REACTOME: PPOX
ConsensusPathDB
Pathway Commons: PPOX
MetabolismMetaCyc: PPOX
HUMANCyc: PPOX
RegulationEnsembl's Regulation: ENSG00000143224
miRBase: chr1 :161,136,180-161,141,010
TargetScan: NM_000309
cisRED: ENSG00000143224
ContextiHOP: PPOX
cancer metabolism search in PubMed: PPOX
UCL Cancer Institute: PPOX
Assigned class in ccmGDBC

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

Mutations for PPOX
* 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 PPOX related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DC302335ELK1287X4750989447509979PPOX875461161144978161146355

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=31)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr1:161138854-161138854p.R230C2
chr1:161139745-161139745p.L306L2
chr1:161136677-161136677p.G14S2
chr1:161138221-161138221p.?2
chr1:161140875-161140875p.G448A2
chr1:161140428-161140428p.W373R2
chr1:161136921-161136921p.G40A1
chr1:161139480-161139480p.D280H1
chr1:161137244-161137244p.G102G1
chr1:161140454-161140454p.G381G1

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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
# sample52 6  1    3131 4414
# mutation62 6  1    3121 4414
nonsynonymous SNV32 5       3111 321 
synonymous SNV3  1  1      1  12 4
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
chr1:161137880p.T145I,PPOX2
chr1:161137200p.G102G,PPOX1
chr1:161138868p.G345R,PPOX1
chr1:161140536p.G111C,PPOX1
chr1:161137223p.G345E,PPOX1
chr1:161138933p.V365V,PPOX1
chr1:161140556p.F149C,PPOX1
chr1:161137244p.G381G,PPOX1
chr1:161138959p.A150T,PPOX1
chr1:161140705p.H409Y,PPOX1

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 PPOX 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 PPOX

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

BOLA1,C1orf35,RRNAD1,CLK2,DPM3,INO80E,KLHDC9,
MRPL55,MTX1,NDUFS2,NIT1,PMF1,PMVK,PPOX,
LAMTOR2,SCAMP3,TSTD1,UFC1,USF1,USP21,ZNF692
ADCK4,ANAPC2,ATG4B,CCDC130,CCDC22,CDK10,CDK5RAP3,
COQ4,CXXC1,FAM98C,FBXO44,GGA1,MOGS,NAT9,
NDOR1,NOL12,OGFOD2,POMT1,PPOX,ZFYVE19,ZNF446

ACBD6,B4GALT3,CLK2,DCAF8,HAX1,JTB,KLHDC9,
LYSMD1,MRPL24,PI4KB,PMF1,PPOX,PSMD4,PYCR2,
RCOR3,LAMTOR2,SCAMP3,SCNM1,UBQLN4,USP21,VPS72
AGBL5,C12orf10,C1orf35,C1orf86,CPNE1,DPP7,DRG2,
EIF3G,GRAMD1A,HEMK1,POLL,PPOX,RGL2,RNF166,
SDR39U1,SNAP47,STK19,TAB1,THAP11,WBP1,WDR83
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 PPOX
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
DB00145protoporphyrinogen oxidaseapproved; nutraceuticalGlycine


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Cross referenced IDs for PPOX
* 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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