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 PSMB10
Basic gene info.Gene symbolPSMB10
Gene nameproteasome (prosome, macropain) subunit, beta type, 10
SynonymsLMP10|MECL1|beta2i
CytomapUCSC genome browser: 16q22.1
Genomic locationchr16 :67968406-67970780
Type of geneprotein-coding
RefGenesNM_002801.3,
Ensembl idENSG00000205220
Descriptionlow molecular mass protein 10macropain subunit MECl-1multicatalytic endopeptidase complex subunit MECl-1proteasome MECl-1proteasome catalytic subunit 2iproteasome subunit MECL1proteasome subunit beta 7iproteasome subunit beta type-10proteasome sub
Modification date20141207
dbXrefs MIM : 176847
HGNC : HGNC
Ensembl : ENSG00000205220
HPRD : 01465
Vega : OTTHUMG00000137553
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMB10
BioGPS: 5699
Gene Expression Atlas: ENSG00000205220
The Human Protein Atlas: ENSG00000205220
PathwayNCI Pathway Interaction Database: PSMB10
KEGG: PSMB10
REACTOME: PSMB10
ConsensusPathDB
Pathway Commons: PSMB10
MetabolismMetaCyc: PSMB10
HUMANCyc: PSMB10
RegulationEnsembl's Regulation: ENSG00000205220
miRBase: chr16 :67,968,406-67,970,780
TargetScan: NM_002801
cisRED: ENSG00000205220
ContextiHOP: PSMB10
cancer metabolism search in PubMed: PSMB10
UCL Cancer Institute: PSMB10
Assigned class in ccmGDBC

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Phenotypic Information for PSMB10(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMB10
Familial Cancer Database: PSMB10
* 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: PSMB10
MedGen: PSMB10 (Human Medical Genetics with Condition)
ClinVar: PSMB10
PhenotypeMGI: PSMB10 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMB10

Mutations for PSMB10
* 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 PSMB10 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE832990FBXW532829139835137139835187PSMB1078133166797032767970383

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=12)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr16:67970307-67970307p.V46V3
chr16:67969929-67969929p.L107fs*312
chr16:67969930-67969930p.L107L2
chr16:67970185-67970185p.A59T2
chr16:67969531-67969531p.G151G2
chr16:67970188-67970188p.R58G2
chr16:67968568-67968568p.G239G2
chr16:67970600-67970600p.Q18P1
chr16:67968708-67968708p.P234P1
chr16:67969920-67969920p.G110D1

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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
# sample   1  2    11   24 3
# mutation   1  3    11   24 3
nonsynonymous SNV      3    1    11 2
synonymous SNV   1        1   13 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
chr16:67968568p.G239G2
chr16:67970203p.A214S1
chr16:67968747p.D213D1
chr16:67970607p.E178K1
chr16:67968770p.L177P1
chr16:67968771p.L122L1
chr16:67969349p.R120S1
chr16:67969351p.A116A1
chr16:67969883p.S108Y1
chr16:67969891p.D56Y1

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 PSMB10 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 PSMB10

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 PSMB10


There's no related Drug.
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Cross referenced IDs for PSMB10
* 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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