Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 PCCB
Basic gene info.Gene symbolPCCB
Gene namepropionyl CoA carboxylase, beta polypeptide
Synonyms-
CytomapUCSC genome browser: 3q21-q22
Genomic locationchr3 :135969166-136049013
Type of geneprotein-coding
RefGenesNM_000532.4,
NM_001178014.1,
Ensembl idENSG00000114054
DescriptionPCCase subunit betapropanoyl-CoA:carbon dioxide ligase subunit betapropionyl Coenzyme A carboxylase, beta polypeptidepropionyl-CoA carboxylase beta chain, mitochondrial
Modification date20141219
dbXrefs MIM : 232050
HGNC : HGNC
Ensembl : ENSG00000114054
HPRD : 01982
Vega : OTTHUMG00000159792
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PCCB
BioGPS: 5096
Gene Expression Atlas: ENSG00000114054
The Human Protein Atlas: ENSG00000114054
PathwayNCI Pathway Interaction Database: PCCB
KEGG: PCCB
REACTOME: PCCB
ConsensusPathDB
Pathway Commons: PCCB
MetabolismMetaCyc: PCCB
HUMANCyc: PCCB
RegulationEnsembl's Regulation: ENSG00000114054
miRBase: chr3 :135,969,166-136,049,013
TargetScan: NM_000532
cisRED: ENSG00000114054
ContextiHOP: PCCB
cancer metabolism search in PubMed: PCCB
UCL Cancer Institute: PCCB
Assigned class in ccmGDBC

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Phenotypic Information for PCCB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PCCB
Familial Cancer Database: PCCB
* 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: PCCB
MedGen: PCCB (Human Medical Genetics with Condition)
ClinVar: PCCB
PhenotypeMGI: PCCB (International Mouse Phenotyping Consortium)
PhenomicDB: PCCB

Mutations for PCCB
* 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 PCCB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM873521PCCB11163136051715136051830PCCB1172143136051900136051997
BM874469PCCB11153136051715136051829PCCB1162133136051900136051997
AU126976RPL3411664109541733109543328PCCB1665703135969191135975471

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 # sample          1      
GAIN (# sample)          1      
LOSS (# sample)                 
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=39)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr3:136048788-136048788p.R514*3
chr3:135975437-135975437p.N115S2
chr3:136046496-136046496p.D440D1
chr3:136012664-136012664p.Q241*1
chr3:135974708-135974708p.T65K1
chr3:136016909-136016909p.D293D1
chr3:136035829-136035829p.K338M1
chr3:136046515-136046515p.L447F1
chr3:136012666-136012666p.Q241H1
chr3:135974715-135974715p.R67S1

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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
# sample12 41 3 5  56   43 9
# mutation12 41 3 5  56   44 10
nonsynonymous SNV 1 41 1 4  36   23 8
synonymous SNV11    2 1  2    21 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
chr3:136019916p.P191H,PCCB2
chr3:136002707p.S310L,PCCB2
chr3:136035827p.F494L,PCCB1
chr3:135974724p.D98V,PCCB1
chr3:136046531p.S322F,PCCB1
chr3:136016830p.A513A,PCCB1
chr3:136035861p.G104E,PCCB1
chr3:135974785p.R327H,PCCB1
chr3:136046553p.R514R,PCCB1
chr3:136016889p.V108V,PCCB1

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 PCCB 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 PCCB

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

ANAPC13,ATPAF1,HMCES,CCDC58,FKBP3,GSTZ1,LSM3,
MRPL3,MRPS22,MRPS33,NDUFB4,NIT2,PCCB,TRMT10C,
RNF7,RUVBL1,SEC22A,SRPRB,TFDP2,UBA5,UMPS
ACADM,AIFM1,ATP5G3,ATPAF1,CS,DLD,ETFA,
ETFDH,FH,GHITM,HIBADH,LDHD,MRPS15,PCCB,
PDHA1,PDHB,ECI2,SDHC,SLC25A23,SLC2A4,SUCLG2

ATP5A1,ATP5B,ATPAF2,C1QBP,C3orf33,COPS3,COQ6,
DLST,ECHS1,EIF5A,ETFA,FAM162A,KIAA0391,MPDU1,
PCCB,PPA2,RNMTL1,SCO1,SLC25A11,TXN2,UQCRC1
ATP5C1,ATP5F1,TEFM,CELA3A,DRD5,DUSP21,IAPP,
INTS7,MGC87042,MRPS28,MRPS35,NDUFB9,NIPSNAP3A,PCCB,
PDHX,PSG1,SLC37A2,SSX8,TMEM211,UQCRFS1,VCY
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 PCCB
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, beta polypeptideapproved; nutraceuticalBiotin
DB00161propionyl CoA carboxylase, beta polypeptideapproved; nutraceuticalL-Valine


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Cross referenced IDs for PCCB
* 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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