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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PCCB |
Basic gene info. | Gene symbol | PCCB |
Gene name | propionyl CoA carboxylase, beta polypeptide | |
Synonyms | - | |
Cytomap | UCSC genome browser: 3q21-q22 | |
Genomic location | chr3 :135969166-136049013 | |
Type of gene | protein-coding | |
RefGenes | NM_000532.4, NM_001178014.1, | |
Ensembl id | ENSG00000114054 | |
Description | PCCase subunit betapropanoyl-CoA:carbon dioxide ligase subunit betapropionyl Coenzyme A carboxylase, beta polypeptidepropionyl-CoA carboxylase beta chain, mitochondrial | |
Modification date | 20141219 | |
dbXrefs | MIM : 232050 | |
HGNC : HGNC | ||
Ensembl : ENSG00000114054 | ||
HPRD : 01982 | ||
Vega : OTTHUMG00000159792 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PCCB | |
BioGPS: 5096 | ||
Gene Expression Atlas: ENSG00000114054 | ||
The Human Protein Atlas: ENSG00000114054 | ||
Pathway | NCI Pathway Interaction Database: PCCB | |
KEGG: PCCB | ||
REACTOME: PCCB | ||
ConsensusPathDB | ||
Pathway Commons: PCCB | ||
Metabolism | MetaCyc: PCCB | |
HUMANCyc: PCCB | ||
Regulation | Ensembl's Regulation: ENSG00000114054 | |
miRBase: chr3 :135,969,166-136,049,013 | ||
TargetScan: NM_000532 | ||
cisRED: ENSG00000114054 | ||
Context | iHOP: PCCB | |
cancer metabolism search in PubMed: PCCB | ||
UCL Cancer Institute: PCCB | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PCCB(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PCCB |
Familial Cancer Database: PCCB |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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: PCCB |
MedGen: PCCB (Human Medical Genetics with Condition) | |
ClinVar: PCCB | |
Phenotype | MGI: 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. |
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 PCCB 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 |
BM873521 | PCCB | 1 | 116 | 3 | 136051715 | 136051830 | PCCB | 117 | 214 | 3 | 136051900 | 136051997 | |
BM874469 | PCCB | 1 | 115 | 3 | 136051715 | 136051829 | PCCB | 116 | 213 | 3 | 136051900 | 136051997 | |
AU126976 | RPL34 | 1 | 166 | 4 | 109541733 | 109543328 | PCCB | 166 | 570 | 3 | 135969191 | 135975471 |
Other DBs for Structural Variants |
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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 |   |   |   |   |   |   |   |   |   |   | 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=39) | (# total SNVs=10) |
(# total SNVs=2) | (# 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 |
chr3:136048788-136048788 | p.R514* | 3 |
chr3:135975437-135975437 | p.N115S | 2 |
chr3:135980854-135980854 | p.A164T | 1 |
chr3:136035898-136035898 | p.V361A | 1 |
chr3:136046553-136046553 | p.E459D | 1 |
chr3:136012687-136012687 | p.K248N | 1 |
chr3:135974739-135974739 | p.D75E | 1 |
chr3:136019907-136019907 | p.P307H | 1 |
chr3:135980900-135980900 | p.I179T | 1 |
chr3:136035904-136035904 | p.S363L | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   | 4 | 1 |   | 3 |   | 5 |   |   | 5 | 6 |   |   |   | 4 | 3 |   | 9 |
# mutation | 1 | 2 |   | 4 | 1 |   | 3 |   | 5 |   |   | 5 | 6 |   |   |   | 4 | 4 |   | 10 |
nonsynonymous SNV |   | 1 |   | 4 | 1 |   | 1 |   | 4 |   |   | 3 | 6 |   |   |   | 2 | 3 |   | 8 |
synonymous SNV | 1 | 1 |   |   |   |   | 2 |   | 1 |   |   | 2 |   |   |   |   | 2 | 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 |
chr3:136019916 | p.P191H,PCCB | 2 |
chr3:136002707 | p.S310L,PCCB | 2 |
chr3:136016895 | p.N536T,PCCB | 1 |
chr3:136035898 | p.I179T,PCCB | 1 |
chr3:135975404 | p.Q358K,PCCB | 1 |
chr3:136048787 | p.V361A,PCCB | 1 |
chr3:136016909 | p.G202G,PCCB | 1 |
chr3:136045650 | p.L366V,PCCB | 1 |
chr3:135975417 | p.K248N,PCCB | 1 |
chr3:136048788 | p.V372V,PCCB | 1 |
Other DBs for Point Mutations |
Copy 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 |
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. |
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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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for PCCB |
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, beta polypeptide | approved; nutraceutical | Biotin | ||
DB00161 | propionyl CoA carboxylase, beta polypeptide | approved; nutraceutical | L-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 |
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