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 PMPCB
Basic gene info.Gene symbolPMPCB
Gene namepeptidase (mitochondrial processing) beta
SynonymsBeta-MPP|MPP11|MPPB|MPPP52|P-52
CytomapUCSC genome browser: 7q22.1
Genomic locationchr7 :102937872-102955133
Type of geneprotein-coding
RefGenesNM_004279.2,
Ensembl idENSG00000105819
Descriptionmitochondrial processing peptidase beta subunitmitochondrial-processing peptidase subunit beta
Modification date20141207
dbXrefs MIM : 603131
HGNC : HGNC
HPRD : 07539
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PMPCB
BioGPS: 9512
Gene Expression Atlas: ENSG00000105819
The Human Protein Atlas: ENSG00000105819
PathwayNCI Pathway Interaction Database: PMPCB
KEGG: PMPCB
REACTOME: PMPCB
ConsensusPathDB
Pathway Commons: PMPCB
MetabolismMetaCyc: PMPCB
HUMANCyc: PMPCB
RegulationEnsembl's Regulation: ENSG00000105819
miRBase: chr7 :102,937,872-102,955,133
TargetScan: NM_004279
cisRED: ENSG00000105819
ContextiHOP: PMPCB
cancer metabolism search in PubMed: PMPCB
UCL Cancer Institute: PMPCB
Assigned class in ccmGDBC

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

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

Mutations for PMPCB
* 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 PMPCB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF229388GOLIM4152093167759219167761317PMPCB2082727102962511102963005
AW838568RPS2466402107979510579797006PMPCB3975017102963027102963201
BE709389PMPCB1992187102967741102967760PCBD22134665134262570134262823
AW838567RPS2452389107979510479797006PMPCB3844887102963027102963201
AI205138ATL11313145109906351099375PMPCB3145147102939038102939972
DA111094ZNF60811735124004429124004600PMPCB1735887102953469102953884
BE929033PRKCH33223146181439861814591PMPCB2212947102940672102940745
AW993843PMPCB24027102956273102960127MAP440363634791257247913556

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=30)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=1)
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
chr7:102944925-102944925p.A242T2
chr7:102939109-102939109p.S65N2
chr7:102949405-102949405p.V286L2
chr7:102949503-102949503p.T318T1
chr7:102940636-102940636p.K113N1
chr7:102952336-102952336p.R441I1
chr7:102948074-102948074p.A256A1
chr7:102950769-102950769p.S334F1
chr7:102940661-102940661p.E122Q1
chr7:102952549-102952549p.Y459S1

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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
# sample1  22 1   1325  23 3
# mutation1  22 1   1325  23 3
nonsynonymous SNV1  22     1225  21 3
synonymous SNV      1    1     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
chr7:102949405p.V286L2
chr7:102948111p.R15Q1
chr7:102940661p.D262H1
chr7:102948151p.R16L1
chr7:102940667p.G269R1
chr7:102949403p.L25V1
chr7:102940676p.S282T1
chr7:102937947p.Q50K1
chr7:102940681p.R285H1
chr7:102950871p.L53L1

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 PMPCB 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 PMPCB

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

AGK,ARMC10,BET1,RBM48,DLD,DNAJC2,DUS4L,
FAM133B,FAM185A,FAM200A,GTPBP10,KRIT1,NAPEPLD,NDUFA5,
ORC5,PMPCB,POT1,RINT1,SPDYE3,ZNF3,ZSCAN25
ABCB7,EIF2A,EIF2S3,EIF3E,EIF3L,EIF3M,EIF4B,
LIAS,MRPL45,NAP1L1,LRRC75A-AS1,PCBP2,PMPCB,POLR1D,
RPL22,RSL1D1,SUPV3L1,TAF1D,TATDN1,TIMM9,TMEM18

ACN9,ARMC10,ATP5J2,BET1,BUD31,C6orf57,COPS6,
DUS4L,FIS1,GBAS,GTPBP10,IMMP2L,MRPS33,NDUFA4,
ORC5,PMPCB,PMS2P1,RHEB,RINT1,SSBP1,ZNF277
ANKRD49,ATG5,ATP5S,C1orf43,COMMD3,DPY30,EBAG9,
EEF1B2,GOLGA7,GPN1,LYPLA1,MKKS,MYNN,NDUFB5,
PEX2,PMPCB,RCHY1,RPS3A,TATDN1,TMEM14B,TMEM14C
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 PMPCB


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