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 PSMB2
Basic gene info.Gene symbolPSMB2
Gene nameproteasome (prosome, macropain) subunit, beta type, 2
SynonymsHC7-I
CytomapUCSC genome browser: 1p34.2
Genomic locationchr1 :36065142-36097138
Type of geneprotein-coding
RefGenesNM_001199779.1,
NM_001199780.1,NM_002794.4,
Ensembl idENSG00000126067
Descriptionmacropain subunit C7-Imulticatalytic endopeptidase complex subunit C7-1multicatalytic endopeptidase complex subunit C7-Iproteasome beta 2 subunitproteasome component C7-Iproteasome subunit beta type-2proteasome subunit, beta type, 2
Modification date20141207
dbXrefs MIM : 602175
HGNC : HGNC
Ensembl : ENSG00000126067
HPRD : 03708
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMB2
BioGPS: 5690
Gene Expression Atlas: ENSG00000126067
The Human Protein Atlas: ENSG00000126067
PathwayNCI Pathway Interaction Database: PSMB2
KEGG: PSMB2
REACTOME: PSMB2
ConsensusPathDB
Pathway Commons: PSMB2
MetabolismMetaCyc: PSMB2
HUMANCyc: PSMB2
RegulationEnsembl's Regulation: ENSG00000126067
miRBase: chr1 :36,065,142-36,097,138
TargetScan: NM_001199779
cisRED: ENSG00000126067
ContextiHOP: PSMB2
cancer metabolism search in PubMed: PSMB2
UCL Cancer Institute: PSMB2
Assigned class in ccmGDBC

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Phenotypic Information for PSMB2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMB2
Familial Cancer Database: PSMB2
* 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: PSMB2
MedGen: PSMB2 (Human Medical Genetics with Condition)
ClinVar: PSMB2
PhenotypeMGI: PSMB2 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMB2

Mutations for PSMB2
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastPSMB2chr13608515536085155chr101521683515216835
ovaryPSMB2chr13609153036091550DLGAP3chr13533584935335869
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PSMB2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE908471SRC1221203603175336031973PSMB220847813606874536070873
AA393815PSMB2123813606855936068796PSMB223451813610192736107120
CB156087PSMB2147213606766936068140SLC25A354676601781934478193640
AA393918PSMB2135013609689636107120PSMB234643013606855936068643

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=9)
Stat. for Synonymous SNVs
(# total SNVs=1)
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
chr1:36101971-36101971p.D52H2
chr1:36101917-36101917p.R70*1
chr1:36070882-36070882p.T150T1
chr1:36074873-36074873p.S141T1
chr1:36102023-36102023p.K34N1
chr1:36074881-36074891p.G135fs*161
chr1:36107026-36107026p.Y3C1
chr1:36074882-36074882p.L138P1
chr1:36074928-36074928p.A123T1
chr1:36074940-36074940p.D119N1

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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   4  1         23 1
# mutation   3  1         23 1
nonsynonymous SNV   2  1         22 1
synonymous SNV   1             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
chr1:36074882p.L21P,PSMB22
chr1:36107026p.S62T,PSMB21
chr1:36068938p.T60I,PSMB21
chr1:36068944p.T33T,PSMB21
chr1:36070882p.S24T,PSMB21
chr1:36074873p.A6T,PSMB21
chr1:36074928p.A89A,PSMB21
chr1:36074953p.R70L,PSMB21
chr1:36096876p.R68W,PSMB21
chr1:36096883p.K12N,PSMB21

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 PSMB2 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 PSMB2

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

ADPRHL2,AK2,AUNIP,CDC20,CDCA8,EIF2B3,ERI3,
GNL2,KIF2C,MAGOH,MED8,MRPL37,PSMB2,PSMG1,
PTTG1,TRAPPC3,TUBA1C,UQCRH,UQCRHL,UTP11L,YARS
CDC123,COX16,DYNLT1,GNG5,MRPL47,MYL12B,NOP10,
NUTF2,PSMA1,PSMA3,PSMA4,PSMA5,PSMB2,RBX1,
RRAGA,SDHAF2,SLC35B1,SNRPG,TOMM5,TOMM6,UCHL3

ACOT7,ADPRHL2,AK2,SMIM12,CDC20,EBNA1BP2,EIF3I,
HDAC1,MRPL20,MRPL37,MRPS15,NOC2L,NUDC,PEF1,
PRDX1,PSMA5,PSMB2,TRAPPC3,TUBA1C,UTP11L,YARS
ACTR3,ASS1,CALR,CRELD2,DDX39A,DNAJB11,EIF5AL1,
ENO1,H2AFZ,MANF,NOS2,PDIA6,PPIB,PSMA3,
PSMB2,PSMB5,PSMC4,RPN1,SDF2L1,SEC61B,SNRPF
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 PSMB2
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, 2approved; investigationalBortezomib
DB07475proteasome (prosome, macropain) subunit, beta type, 2experimentalN-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB08515proteasome (prosome, macropain) subunit, beta type, 2experimental(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, 2approved; nutraceuticalAdenosine triphosphate


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Cross referenced IDs for PSMB2
* 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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