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 PSMB6
Basic gene info.Gene symbolPSMB6
Gene nameproteasome (prosome, macropain) subunit, beta type, 6
SynonymsDELTA|LMPY|Y
CytomapUCSC genome browser: 17p13
Genomic locationchr17 :4699456-4701790
Type of geneprotein-coding
RefGenesNM_001270481.1,
NM_002798.2,
Ensembl idENSG00000142507
DescriptionPSY large multifunctional protease Ymacropain delta chainmulticatalytic endopeptidase complex delta chainproteasome catalytic subunit 1proteasome delta chainproteasome subunit Yproteasome subunit beta type-6proteasome subunit delta
Modification date20141207
dbXrefs MIM : 600307
HGNC : HGNC
Ensembl : ENSG00000142507
HPRD : 02630
Vega : OTTHUMG00000090777
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMB6
BioGPS: 5694
Gene Expression Atlas: ENSG00000142507
The Human Protein Atlas: ENSG00000142507
PathwayNCI Pathway Interaction Database: PSMB6
KEGG: PSMB6
REACTOME: PSMB6
ConsensusPathDB
Pathway Commons: PSMB6
MetabolismMetaCyc: PSMB6
HUMANCyc: PSMB6
RegulationEnsembl's Regulation: ENSG00000142507
miRBase: chr17 :4,699,456-4,701,790
TargetScan: NM_001270481
cisRED: ENSG00000142507
ContextiHOP: PSMB6
cancer metabolism search in PubMed: PSMB6
UCL Cancer Institute: PSMB6
Assigned class in ccmGDBC

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Phenotypic Information for PSMB6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMB6
Familial Cancer Database: PSMB6
* 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_AMINO_ACIDS_AND_DERIVATIVES
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PSMB6
MedGen: PSMB6 (Human Medical Genetics with Condition)
ClinVar: PSMB6
PhenotypeMGI: PSMB6 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMB6

Mutations for PSMB6
* 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 PSMB6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CN430188PSMB614991746994744701354ANKRD27495646193309516933095320

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
There's no copy number variation information in COSMIC data for this gene.

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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=12)
Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr17:4700797-4700797p.R79C1
chr17:4701345-4701345p.S158S1
chr17:4699490-4699490p.M1V1
chr17:4700837-4700837p.A92V1
chr17:4701402-4701402p.Y177Y1
chr17:4699552-4699552p.A21A1
chr17:4700982-4700982p.E103G1
chr17:4701416-4701416p.T182N1
chr17:4700075-4700075p.S52F1
chr17:4700983-4700983p.E103E1

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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
# sample1215  1    1121 12 5
# mutation1214  1    1121 12 5
nonsynonymous SNV12 2  1    1111 11 3
synonymous SNV  12         1   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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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
chr17:4700837p.A92V,PSMB62
chr17:4701048p.V40M,PSMB61
chr17:4701657p.G165G,PSMB61
chr17:4700038p.S52F,PSMB61
chr17:4701064p.T182N,PSMB61
chr17:4700075p.Y59H,PSMB61
chr17:4701076p.G207R,PSMB61
chr17:4700737p.N62K,PSMB61
chr17:4701090p.L210L1
chr17:4700748p.R63Q,PSMB61

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 PSMB6 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 PSMB6

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

C17orf49,EIF5A,GADD45GIP1,GPS2,NAA38,MED11,NDUFA13,
NDUFB8,OVCA2,PELP1,PFN1,PSMB6,RNASEK,RNMTL1,
SLC25A11,SPAG7,TIMM22,EMC6,TRAPPC1,TXNDC17,WRAP53
AKT1S1,ANAPC11,BABAM1,C19orf70,COPS6,FAM89B,FIS1,
GPS1,LSM10,MRPL2,NDUFA13,NDUFB7,NDUFS6,NDUFS8,
NOSIP,PARK7,PSMB5,PSMB6,PSMC3,PSMD4,STUB1

ATPAF2,ELP5,DERL2,CTDNEP1,EIF4A1,EIF5A,EIF5AL1,
ELAC2,NAA38,MED11,MPDU1,OVCA2,PFN1,PSMB6,
RNASEK,RNMTL1,SLC25A11,TIMM22,EMC6,TXNDC17,WRAP53
DPCD,ENSA,LSM3,NEDD8,NUBP1,PARK7,PGAM1,
POLR2L,PSMA3,PSMA7,PSMB1,PSMB4,PSMB5,PSMB6,
PSMB7,PSMC2,PSMC3,PSMD13,PSMD4,PSMD7,SSSCA1
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 PSMB6
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
DB07475proteasome (prosome, macropain) subunit, beta type, 6experimentalN-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB08515proteasome (prosome, macropain) subunit, beta type, 6experimental(3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE
DB00171proteasome (prosome, macropain) subunit, beta type, 6approved; nutraceuticalAdenosine triphosphate


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Cross referenced IDs for PSMB6
* 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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