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 PCCA

Basic gene info.	Gene symbol	PCCA
	Gene name	propionyl CoA carboxylase, alpha polypeptide
	Synonyms	-
	Cytomap	UCSC genome browser: 13q32
	Genomic location	chr13 :100741268-101182691
	Type of gene	protein-coding
	RefGenes	NM_000282.3, NM_001127692.2,NM_001178004.1,
	Ensembl id	ENSG00000175198
	Description	PCCase alpha subunitpccA complementation grouppropanoyl-CoA:carbon dioxide ligase alpha subunitpropionyl Coenzyme A carboxylase, alpha polypeptidepropionyl-CoA carboxylase alpha chain, mitochondrial
	Modification date	20141219
dbXrefs	MIM : 232000
	HGNC : HGNC
	Ensembl : ENSG00000175198
	HPRD : 01981
	Vega : OTTHUMG00000017284
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PCCA
	BioGPS: 5095
	Gene Expression Atlas: ENSG00000175198
	The Human Protein Atlas: ENSG00000175198
Pathway	NCI Pathway Interaction Database: PCCA
	KEGG: PCCA
	REACTOME: PCCA
	ConsensusPathDB
	Pathway Commons: PCCA
Metabolism	MetaCyc: PCCA
	HUMANCyc: PCCA
Regulation	Ensembl's Regulation: ENSG00000175198
	miRBase: chr13 :100,741,268-101,182,691
	TargetScan: NM_000282
	cisRED: ENSG00000175198
Context	iHOP: PCCA
	cancer metabolism search in PubMed: PCCA
	UCL Cancer Institute: PCCA
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: PCCA
	Familial Cancer Database: PCCA

* 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
KEGG_PROPANOATE_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

Mutations for PCCA

* 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

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
central_nervous_system	PCCA	chr13	100767216	100767216	NALCN-AS1	chr13	101694698	101694698
ovary	PCCA	chr13	100756606	100756626	PCCA	chr13	100757471	100757491
ovary	PCCA	chr13	100759511	100759531		chr24	14490479	14490499
ovary	PCCA	chr13	100759511	100759531	ARSD	chr23	2837178	2837198
pancreas	PCCA	chr13	101161434	101161454	PCCA	chr13	101153573	101153593

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 PCCA 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
AI951320	PCNP	28	83	3	101313224	101313279	PCCA	78	525	13	100809560	100921006
BE071691	PCCA	14	445	13	100818025	100818454	PCCA	434	612	13	100820153	100820334
BF811509	MALAT1	11	368	11	65271972	65272331	PCCA	363	430	13	101171483	101171550
BE071684	PCCA	6	438	13	100818025	100818455	PCCA	427	601	13	100820153	100820328
BG980943	PCCA	1	131	13	101119337	101119477	SERPINE1	118	388	7	100778865	100780774

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

Mutation type/ Tissue ID	brca	cns	cerv	endome	haematopo	kidn	Lintest	liver	lung	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	4	1		1			2				2		1		1
GAIN (# sample)	4	1		1			1				1				1
LOSS (# sample)							1				1		1

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=54)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=1)

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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
chr13:100909900-100909900	p.R230H	6
chr13:101077939-101077939	p.S600L	3
chr13:100809577-100809577	p.E151*	3
chr13:101077972-101077972	p.Q611L	3
chr13:101020767-101020767	p.S562L	3
chr13:101020796-101020796	p.V572I	3
chr13:100953816-100953816	p.R390C	2
chr13:100809554-100809554	p.Y143C	2
chr13:101077983-101077983	p.Q615K	2
chr13:100861692-100861692	p.I192N	2

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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=5

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		15	2		4		2			7	2	1			8	8	1	6
# mutation		2		16	2		4		2			8	2	1			8	5	1	7
nonsynonymous SNV		1		13	2		4		2			7	2	1			4	5		5
synonymous SNV		1		3								1					4		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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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
chr13:100909900	p.R204H,PCCA	5
chr13:100915005	p.Q221E,PCCA	2
chr13:101077904	p.F311F,PCCA	1
chr13:100953732	p.H454Y,PCCA	1
chr13:100962160	p.I661M,PCCA	1
chr13:100807338	p.G116C,PCCA	1
chr13:100915016	p.F321L,PCCA	1
chr13:101077918	p.I464I,PCCA	1
chr13:100953772	p.T680T,PCCA	1
chr13:100982823	p.Y117C,PCCA	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 PCCA 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 PCCA

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


ABHD13,ALDH6A1,CARKD,CLN5,COG3,COG6,CUL4A, DNAJC3,DOCK9,ERCC5,FBXL3,VWA8,NDFIP2,PCCA, PIBF1,SUCLA2,TM9SF2,TMCO3,TMTC4,TRIM68,VPS36	ABHD15,ACACB,ACSS3,ACVR1C,ADH1B,ALDH6A1,BNIP3L, RHOV___CHP1,CYB5A,GHR,GYG2,HADH,IDH1,LGALS12, LOC283392,MARC1,MARC2,OXCT1,PCCA,PECR,PEX19

ADAM2,C2CD4B,CACNB4,CCDC33,FAM133A,GIF,GP9, IL19,JSRP1,KLK1,KLK3,MYO3B,PAGE1,PCCA, RASD1,SPINK4,TFF3,TPH1,TPSG1,WFDC2,ZG16	ADH1C,ATP5A1,B4GALNT2,BCKDHB,APMAP,FAM45A,FAM45B, GJB1,HADH,IGFBP2,LRPPRC,MEST,METAP1,NDUFA10, PCCA,PCCB,PITX2,SDR42E1,SUCLG2,SUPV3L1,TBRG4

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 PCCA

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00121	propionyl CoA carboxylase, alpha polypeptide	approved; nutraceutical	Biotin

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Cross referenced IDs for PCCA

* 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