Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	PMPCB
	Gene name	peptidase (mitochondrial processing) beta
	Synonyms	Beta-MPP\|MPP11\|MPPB\|MPPP52\|P-52
	Cytomap	UCSC genome browser: 7q22.1
	Genomic location	chr7 :102937872-102955133
	Type of gene	protein-coding
	RefGenes	NM_004279.2,
	Ensembl id	ENSG00000105819
	Description	mitochondrial processing peptidase beta subunitmitochondrial-processing peptidase subunit beta
	Modification date	20141207
dbXrefs	MIM : 603131
	HGNC : HGNC
	HPRD : 07539
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PMPCB
	BioGPS: 9512
	Gene Expression Atlas: ENSG00000105819
	The Human Protein Atlas: ENSG00000105819
Pathway	NCI Pathway Interaction Database: PMPCB
	KEGG: PMPCB
	REACTOME: PMPCB
	ConsensusPathDB
	Pathway Commons: PMPCB
Metabolism	MetaCyc: PMPCB
	HUMANCyc: PMPCB
Regulation	Ensembl's Regulation: ENSG00000105819
	miRBase: chr7 :102,937,872-102,955,133
	TargetScan: NM_004279
	cisRED: ENSG00000105819
Context	iHOP: PMPCB
	cancer metabolism search in PubMed: PMPCB
	UCL Cancer Institute: PMPCB
Assigned class in ccmGDB	C

Top

Phenotypic Information for PMPCB(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: PMPCB
	MedGen: PMPCB (Human Medical Genetics with Condition)
	ClinVar: PMPCB
Phenotype	MGI: PMPCB (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PMPCB related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BF229388	GOLIM4	15	209	3	167759219	167761317	PMPCB	208	272	7	102962511	102963005
AW838568	RPS24	66	402	10	79795105	79797006	PMPCB	397	501	7	102963027	102963201
BE709389	PMPCB	199	218	7	102967741	102967760	PCBD2	213	466	5	134262570	134262823
AW838567	RPS24	52	389	10	79795104	79797006	PMPCB	384	488	7	102963027	102963201
AI205138	ATL1	1	313	14	51099063	51099375	PMPCB	314	514	7	102939038	102939972
DA111094	ZNF608	1	173	5	124004429	124004600	PMPCB	173	588	7	102953469	102953884
BE929033	PRKCH	33	223	14	61814398	61814591	PMPCB	221	294	7	102940672	102940745
AW993843	PMPCB	2	402	7	102956273	102960127	MAP4	403	636	3	47912572	47913556

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

There's no copy number variation information in COSMIC data for this gene.

Top

SNV 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

Top

Somatic 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.

Top

Top 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 position	Mutation(aa)	Unique sampleID count
chr7:102939109-102939109	p.S65N	2
chr7:102949405-102949405	p.V286L	2
chr7:102944925-102944925	p.A242T	2
chr7:102944306-102944306	p.D159N	1
chr7:102948151-102948151	p.S282T	1
chr7:102952095-102952095	p.R387Q	1
chr7:102939074-102939074	p.L53L	1
chr7:102944373-102944373	p.E181V	1
chr7:102949403-102949403	p.R285H	1
chr7:102952114-102952114	p.T393T	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1			2	2		1				1	3	2	5			2	3		3
# mutation	1			2	2		1				1	3	2	5			2	3		3
nonsynonymous SNV	1			2	2						1	2	2	5			2	1		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])

Top

Top 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 Position	Mutation(aa)	Unique sampleID count
chr7:102949405	p.V286L	2
chr7:102944925	p.S282T	1
chr7:102939063	p.L25V	1
chr7:102948078	p.R285H	1
chr7:102939074	p.Q50K	1
chr7:102948086	p.L53L	1
chr7:102939894	p.V368A	1
chr7:102948090	p.G82V	1
chr7:102940636	p.T390T	1
chr7:102948111	p.K113N	1

Other 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

Copy 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]

Top

Gene Expression for PMPCB

Gene 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.

Differential 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

CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

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

Top

Pharmacological Information for PMPCB

There's no related Drug.

Top

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