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 PSMB1
Basic gene info.Gene symbolPSMB1
Gene nameproteasome (prosome, macropain) subunit, beta type, 1
SynonymsHC5|PMSB1|PSC5
CytomapUCSC genome browser: 6q27
Genomic locationchr6 :170844203-170862417
Type of geneprotein-coding
RefGenesNM_002793.3,
Ensembl idENSG00000008018
Descriptionmacropain subunit C5multicatalytic endopeptidase complex subunit C5proteasome beta 1 subunitproteasome component C5proteasome gamma chainproteasome subunit HC5proteasome subunit beta type-1
Modification date20141207
dbXrefs MIM : 602017
HGNC : HGNC
Ensembl : ENSG00000008018
HPRD : 03603
Vega : OTTHUMG00000016087
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMB1
BioGPS: 5689
Gene Expression Atlas: ENSG00000008018
The Human Protein Atlas: ENSG00000008018
PathwayNCI Pathway Interaction Database: PSMB1
KEGG: PSMB1
REACTOME: PSMB1
ConsensusPathDB
Pathway Commons: PSMB1
MetabolismMetaCyc: PSMB1
HUMANCyc: PSMB1
RegulationEnsembl's Regulation: ENSG00000008018
miRBase: chr6 :170,844,203-170,862,417
TargetScan: NM_002793
cisRED: ENSG00000008018
ContextiHOP: PSMB1
cancer metabolism search in PubMed: PSMB1
UCL Cancer Institute: PSMB1
Assigned class in ccmGDBC

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Phenotypic Information for PSMB1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMB1
Familial Cancer Database: PSMB1
* 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: PSMB1
MedGen: PSMB1 (Human Medical Genetics with Condition)
ClinVar: PSMB1
PhenotypeMGI: PSMB1 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMB1

Mutations for PSMB1
* 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 PSMB1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CB122525ZFAND61115158035203780352151PSMB11135936170844443170858204
DA076564CDYL21139168083767480837812PSMB11375666170846322170858204
DB153796BCLAF111346136610851136610984PSMB11315776170854940170858205
BG978110GSTP127204116735217067352713PSMB12054596170855254170862345
BG272210PSMB172346170844210170844437GPBP123140755654537156546923
BE122757CSDA1179121085665510862592PSMB11763936170844386170846431

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=11)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr6:170844433-170844433p.R201W3
chr6:170862300-170862300p.P11A3
chr6:170855238-170855238p.H86Y1
chr6:170855244-170855244p.G84S1
chr6:170844489-170844489p.G182D1
chr6:170858099-170858099p.Y72*1
chr6:170844498-170844498p.?1
chr6:170858120-170858120p.T65T1
chr6:170846342-170846342p.Q174E1
chr6:170858188-170858188p.I43F1

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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
# sample2  2     1 4 1  32 3
# mutation2  2     1 4 1  32 3
nonsynonymous SNV2        1 2 1  1  2
synonymous SNV   2       2    22 1
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
chr6:170858120p.I138I1
chr6:170844377p.N107T1
chr6:170858188p.H86Y1
chr6:170844433p.G84S1
chr6:170862291p.T65T1
chr6:170846342p.I43I1
chr6:170862293p.D14H1
chr6:170846364p.R13K1
chr6:170862307p.I225V1
chr6:170846365p.Y8Y1

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 PSMB1 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 PSMB1

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

CCM2,COX4I1,CYBA,EFHD2,FLT3LG,GUK1,HCST,
IRF3,LIME1,LOC606724,LST1,PSMB10,PSMB8,PSMB9,
PSME2,RHOG,RNF166,IGFLR1,TRADD,TYMP,VAMP5
BAX,COPE,CYBA,GALK1,IFI27L2,MBD3,NPDC1,
PLSCR3,PSMB10,PYCARD,RALY,RBM42,RGS19,SCO2,
SHKBP1,SIPA1,SIRT6,SNAPC2,SSBP4,TBCB,ZDHHC12

APOL2,BAK1,BATF2,ETV7,FBXO6,HLA-DMA,IFI35,
IL15RA,IL32,IRF1,NMI,ODF3B,PSMB10,PSMB8,
PSMB9,PSME1,PSME2,RARRES3,SCO2,TAP1,UBE2L6
BATF2,CARD16,EPSTI1,ETV7,FAM26F,GZMB,IFI30,
IFI35,IRF1,PARP9,PSMB10,PSMB8,PSMB9,PSME1,
PSME2,RARRES3,STAT1,TAP1,TRIM21,TYMP,UBE2L6
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 PSMB1
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
DB00188proteasome (prosome, macropain) subunit, beta type, 1approved; investigationalBortezomib
DB07475proteasome (prosome, macropain) subunit, beta type, 1experimentalN-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB08515proteasome (prosome, macropain) subunit, beta type, 1experimental(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, 1approved; nutraceuticalAdenosine triphosphate


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Cross referenced IDs for PSMB1
* 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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