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

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 PMPCA

Basic gene info.	Gene symbol	PMPCA
	Gene name	peptidase (mitochondrial processing) alpha
	Synonyms	Alpha-MPP\|INPP5E\|P-55
	Cytomap	UCSC genome browser: 9q34.3
	Genomic location	chr9 :139305115-139318213
	Type of gene	protein-coding
	RefGenes	NM_001282944.1, NM_001282946.1,NM_015160.2,
	Ensembl id	ENSG00000165688
	Description	inositol polyphosphate-5-phosphatase, 72 kDmitochondrial matrix processing protease, alpha subunitmitochondrial-processing peptidase subunit alpha
	Modification date	20141207
dbXrefs	MIM : 613036
	HGNC : HGNC
	Ensembl : ENSG00000165688
	HPRD : 07500
	Vega : OTTHUMG00000020926
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PMPCA
	BioGPS: 23203
	Gene Expression Atlas: ENSG00000165688
	The Human Protein Atlas: ENSG00000165688
Pathway	NCI Pathway Interaction Database: PMPCA
	KEGG: PMPCA
	REACTOME: PMPCA
	ConsensusPathDB
	Pathway Commons: PMPCA
Metabolism	MetaCyc: PMPCA
	HUMANCyc: PMPCA
Regulation	Ensembl's Regulation: ENSG00000165688
	miRBase: chr9 :139,305,115-139,318,213
	TargetScan: NM_001282944
	cisRED: ENSG00000165688
Context	iHOP: PMPCA
	cancer metabolism search in PubMed: PMPCA
	UCL Cancer Institute: PMPCA
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: PMPCA
	Familial Cancer Database: PMPCA

* 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: PMPCA
	MedGen: PMPCA (Human Medical Genetics with Condition)
	ClinVar: PMPCA
Phenotype	MGI: PMPCA (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PMPCA

Mutations for PMPCA

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_b

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PMPCA 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
BF742243	RILPL1	29	104	12	123984026	124008060	PMPCA	97	221	9	139317869	139317993
BF742244	PMPCA	2	54	9	139317869	139317921	RILPL1	47	141	12	123984008	124008060
BF155162	RILPL1	8	81	12	123984030	124008060	PMPCA	74	198	9	139317869	139317993
BE937971	BOLA2	16	246	16	30129814	30133330	PMPCA	243	339	9	139316289	139316385
M78956	PMPCA	1	250	9	139317962	139318212	GATAD2A	250	311	19	19619679	19619740

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=29)	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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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
chr9:139311437-139311437	p.R223H	2
chr9:139306568-139306568	p.K64R	2
chr9:139317605-139317605	p.P489P	2
chr9:139317629-139317629	p.L497L	2
chr9:139316390-139316390	p.R457L	2
chr9:139310805-139310805	p.P199S	2
chr9:139306464-139306464	p.A29A	1
chr9:139313014-139313014	p.D333A	1
chr9:139309033-139309033	p.D156N	1
chr9:139317583-139317583	p.S482F	1

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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	2	2		2	2		3		1			1	4	2			5	6		6
# mutation	2	2		2	2		3		1			1	4	2			5	6		6
nonsynonymous SNV	2	2		2	1		3		1			1	2	2			2	5		6
synonymous SNV					1								2				3	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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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
chr9:139311437	p.R92H,PMPCA	2
chr9:139309033	p.D56N,PMPCA	2
chr9:139311657	p.A29A	1
chr9:139306464	p.A378T,PMPCA	1
chr9:139317663	p.T67A	1
chr9:139309088	p.V125V,PMPCA	1
chr9:139311661	p.R77C	1
chr9:139306576	p.K138N,PMPCA	1
chr9:139310781	p.S80F	1
chr9:139312525	p.A150T,PMPCA	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 PMPCA 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 PMPCA

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))

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CNV 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

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


C9orf114,C9orf142,C9orf69,RABL6,NELFB,EDF1,FBXW5, NTMT1,MRPS2,PMPCA,PTGES2,REXO4,SDCCAG3,SNAPC4, SSNA1,SURF2,SURF6,TRAF2,UBAC1,DPH7,ZMYND19	ADRM1,DHPS,ECSIT,FAM195A,FASTK,HSF1,MAP2K2, NTMT1,MRPL12,MRPL38,NDUFV1,NSUN5,PMPCA,PTGES2, RNMTL1,SDR39U1,TBRG4,THAP4,TIMM17B,TIMM44,TMED1

ARPC5L,AURKAIP1,C9orf142,COQ4,ENDOG,EXOSC2,FPGS, NTMT1,MRPL41,MRPS2,PMPCA,PSMB7,PTGES2,SDCCAG3, SSNA1,TMEM203,TRUB2,TUBB4B,UBAC1,URM1,ZMYND19	C7orf26,CECR5,DDX28,ELK1,FBXW9,DANCR,LOC348926, MARS2,MRPL12,MRPL4,MRPS12,MRPS2,PMPCA,QTRT1, RCL1,RNMTL1,SFXN4,TIMM13,TRIM27,WDR74,ZMYND19

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

: Open all plots for all cancer types

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Interacting 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 PMPCA

There's no related Drug.

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Cross referenced IDs for PMPCA

* 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