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 ATP5B
Basic gene info.Gene symbolATP5B
Gene nameATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide
SynonymsATPMB|ATPSB|HEL-S-271
CytomapUCSC genome browser: 12q13.13
Genomic locationchr12 :57031958-57039852
Type of geneprotein-coding
RefGenesNM_001686.3,
Ensembl idENSG00000110955
DescriptionATP synthase subunit beta, mitochondrialepididymis secretory protein Li 271mitochondrial ATP synthase beta subunitmitochondrial ATP synthetase, beta subunit
Modification date20141207
dbXrefs MIM : 102910
HGNC : HGNC
Ensembl : ENSG00000110955
HPRD : 00044
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ATP5B
BioGPS: 506
Gene Expression Atlas: ENSG00000110955
The Human Protein Atlas: ENSG00000110955
PathwayNCI Pathway Interaction Database: ATP5B
KEGG: ATP5B
REACTOME: ATP5B
ConsensusPathDB
Pathway Commons: ATP5B
MetabolismMetaCyc: ATP5B
HUMANCyc: ATP5B
RegulationEnsembl's Regulation: ENSG00000110955
miRBase: chr12 :57,031,958-57,039,852
TargetScan: NM_001686
cisRED: ENSG00000110955
ContextiHOP: ATP5B
cancer metabolism search in PubMed: ATP5B
UCL Cancer Institute: ATP5B
Assigned class in ccmGDBC

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Phenotypic Information for ATP5B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ATP5B
Familial Cancer Database: ATP5B
* 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
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ATP5B
MedGen: ATP5B (Human Medical Genetics with Condition)
ClinVar: ATP5B
PhenotypeMGI: ATP5B (International Mouse Phenotyping Consortium)
PhenomicDB: ATP5B

Mutations for ATP5B
* 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 ATP5B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CA312538ATP5B1886125703196257032030ATP5B83135125703202957032081
AW852155ATP5B2185125703360357033790PTGES3184264125707611557076316
AW375766HADH82904108955685108955967ATP5B285399125703196257032076
BE676351ATP5B14124125703196257032072MSI2111443175572335355723686
BF819282ATP5B7105125703659957037268CLU10227182746254227462711
AA128804UBE2T1561202304725202304780ATP5B48107125703196257032021
CV344647ATP5B32425125703727357038740PTMA4215272232573311232573417
BG258137ATP5B29305125703652357037370ATP5B297402125703195957032064
AK127078FMN113310153306573733359029ATP5B33053812125703196257033823
BG179093ATP5B14122125703303357033812ATP5B118539125703196257033065

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=37)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr12:57038968-57038968p.V99V2
chr12:57037687-57037687p.E181Q2
chr12:57033832-57033832p.I407V2
chr12:57033894-57033894p.S386L2
chr12:57036523-57036523p.D295D2
chr12:57039674-57039674p.S25L2
chr12:57038681-57038681p.Q123H2
chr12:57037665-57037665p.K188R2
chr12:57036289-57036289p.Q343*1
chr12:57038732-57038732p.S106S1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21 101   2  523  29 7
# mutation21 101   2  622  39 8
nonsynonymous SNV11 71   1  321  34 5
synonymous SNV1  3    1  3 1   5 3
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
chr12:57033004p.K459Q3
chr12:57036523p.D295D2
chr12:57038968p.V99V2
chr12:57037270p.G237S1
chr12:57039026p.S386L1
chr12:57033775p.A224T1
chr12:57036324p.V384V1
chr12:57037309p.I187I1
chr12:57039070p.F507L1
chr12:57033788p.T375M1

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 ATP5B 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 ATP5B

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

ATP5B,ATP5G3,CCT7,CS,GOT1,HSPA8,HSPA9,
IMMT,MARS,MDH2,PA2G4,PGAM1,PRIM1,PTGES3,
RACGAP1,RAN,SDHB,SHMT2,SLC25A3,SLC25A5,TIMELESS
ACAT1,ACO2,ALPK3,ATP5A1,ATP5B,ADCK3,CHCHD3,
COX5A,FH,GYS1,HADHB,IMMT,MLYCD,NDUFS1,
OGDH,PDHX,SDHA,SDHB,SLC2A4,UQCRC2,UQCRFS1

ATP5A1,ATP5B,C1QBP,COX6A1,CS,DLST,GAPDH,
GOT1,IMMT,ME2,PCCB,PHB2,PSMD9,SCO1,
SDHB,SHMT2,SLC25A3,TPI1,TSFM,TUBA1B,UQCRC1
ATP5A1,ATP5B,ATP5G3,C2orf47,COX5A,DBI,ETFA,
GHITM,GOT1,HARBI1,HCCS,MYCBP,NDUFA9,NDUFS3,
PSMD3,RTN4IP1,SCO1,SQRDL,UQCRC1,UQCRC2,UQCRFS1
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 ATP5B
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
DB04216ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptideexperimentalQuercetin
DB07384ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptideexperimental1-ACETYL-2-CARBOXYPIPERIDINE
DB07394ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptideexperimentalAUROVERTIN B
DB08399ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptideexperimentalPICEATANNOL
DB08629ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptideexperimentalN1-(2-AMINO-4-METHYLPENTYL)OCTAHYDRO-PYRROLO[1,2-A] PYRIMIDINE


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Cross referenced IDs for ATP5B
* 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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