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 symbolPCCA
Gene namepropionyl CoA carboxylase, alpha polypeptide
Synonyms-
CytomapUCSC genome browser: 13q32
Genomic locationchr13 :100741268-101182691
Type of geneprotein-coding
RefGenesNM_000282.3,
NM_001127692.2,NM_001178004.1,
Ensembl idENSG00000175198
DescriptionPCCase alpha subunitpccA complementation grouppropanoyl-CoA:carbon dioxide ligase alpha subunitpropionyl Coenzyme A carboxylase, alpha polypeptidepropionyl-CoA carboxylase alpha chain, mitochondrial
Modification date20141219
dbXrefs MIM : 232000
HGNC : HGNC
Ensembl : ENSG00000175198
HPRD : 01981
Vega : OTTHUMG00000017284
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PCCA
BioGPS: 5095
Gene Expression Atlas: ENSG00000175198
The Human Protein Atlas: ENSG00000175198
PathwayNCI Pathway Interaction Database: PCCA
KEGG: PCCA
REACTOME: PCCA
ConsensusPathDB
Pathway Commons: PCCA
MetabolismMetaCyc: PCCA
HUMANCyc: PCCA
RegulationEnsembl's Regulation: ENSG00000175198
miRBase: chr13 :100,741,268-101,182,691
TargetScan: NM_000282
cisRED: ENSG00000175198
ContextiHOP: PCCA
cancer metabolism search in PubMed: PCCA
UCL Cancer Institute: PCCA
Assigned class in ccmGDBC

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Phenotypic Information for PCCA(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_PROPANOATE_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
central_nervous_systemPCCAchr13100767216100767216NALCN-AS1chr13101694698101694698
ovaryPCCAchr13100756606100756626PCCAchr13100757471100757491
ovaryPCCAchr13100759511100759531chr241449047914490499
ovaryPCCAchr13100759511100759531ARSDchr2328371782837198
pancreasPCCAchr13101161434101161454PCCAchr13101153573101153593
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PCCA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI951320PCNP28833101313224101313279PCCA7852513100809560100921006
BE071691PCCA1444513100818025100818454PCCA43461213100820153100820334
BF811509MALAT111368116527197265272331PCCA36343013101171483101171550
BE071684PCCA643813100818025100818455PCCA42760113100820153100820328
BG980943PCCA113113101119337101119477SERPINE11183887100778865100780774

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample41 1  2   2 1 1  
GAIN (# sample)41 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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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=6

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check002.gifSomatic 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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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
chr13:100909900-100909900p.R230H6
chr13:101020796-101020796p.V572I3
chr13:101077939-101077939p.S600L3
chr13:100809577-100809577p.E151*3
chr13:101077972-101077972p.Q611L3
chr13:101020767-101020767p.S562L3
chr13:100925452-100925452p.L308fs*142
chr13:100953816-100953816p.R390C2
chr13:100809554-100809554p.Y143C2
chr13:101077983-101077983p.Q615K2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 152 4 2  721  8816
# mutation 2 162 4 2  821  8517
nonsynonymous SNV 1 132 4 2  721  45 5
synonymous SNV 1 3       1    4 12
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
chr13:100909900p.R204H,PCCA5
chr13:100915005p.Q221E,PCCA2
chr13:100914983p.A183T,PCCA1
chr13:101020796p.E336K,PCCA1
chr13:100925585p.K487R,PCCA1
chr13:101182352p.G197C,PCCA1
chr13:100807321p.R349P,PCCA1
chr13:100959453p.S536L,PCCA1
chr13:100914988p.R357R,PCCA1
chr13:101077896p.V537V,PCCA1

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 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

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

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
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 PCCA
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
DB00121propionyl CoA carboxylase, alpha polypeptideapproved; nutraceuticalBiotin


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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



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