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 PSMB7
Basic gene info.Gene symbolPSMB7
Gene nameproteasome (prosome, macropain) subunit, beta type, 7
SynonymsZ
CytomapUCSC genome browser: 9q34.11-q34.12
Genomic locationchr9 :127115743-127177721
Type of geneprotein-coding
RefGenesNM_002799.3,
Ensembl idENSG00000136930
Descriptionmacropain chain Zmulticatalytic endopeptidase complex chain Zproteasome catalytic subunit 2proteasome subunit Zproteasome subunit alphaproteasome subunit beta type-7
Modification date20141207
dbXrefs MIM : 604030
HGNC : HGNC
Ensembl : ENSG00000136930
HPRD : 04940
Vega : OTTHUMG00000021042
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMB7
BioGPS: 5695
Gene Expression Atlas: ENSG00000136930
The Human Protein Atlas: ENSG00000136930
PathwayNCI Pathway Interaction Database: PSMB7
KEGG: PSMB7
REACTOME: PSMB7
ConsensusPathDB
Pathway Commons: PSMB7
MetabolismMetaCyc: PSMB7
HUMANCyc: PSMB7
RegulationEnsembl's Regulation: ENSG00000136930
miRBase: chr9 :127,115,743-127,177,721
TargetScan: NM_002799
cisRED: ENSG00000136930
ContextiHOP: PSMB7
cancer metabolism search in PubMed: PSMB7
UCL Cancer Institute: PSMB7
Assigned class in ccmGDBC

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Phenotypic Information for PSMB7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMB7
Familial Cancer Database: PSMB7
* 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: PSMB7
MedGen: PSMB7 (Human Medical Genetics with Condition)
ClinVar: PSMB7
PhenotypeMGI: PSMB7 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMB7

Mutations for PSMB7
* 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
There's no inter-chromosomal structural variation.
- 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
skinPSMB7chr9127118224127118224chr9128022004128022004
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 PSMB7 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ925563PSMB716079127119210127119816EEF1D6088558144668389144679566
DA677584PSMB744129127174629127177716SMEK1409549149195199291957148
W23061PSMB7133659127174680127177711PSMB73585179127167596127174681
AA488934KDM5C1159X5322137853221536PSMB71553709127115749127115964
AI638157SMYD5119027345416273454351PSMB71875169127150948127151277
AW449088FUS15306163120234731202926PSMB73044149127116963127117073
BQ424626PSMB7162649127176187127177699PSMB72646939127119052127174738
BF831316DCTN47965150112318150112409PSMB7813719127120646127120937
BM990034PSMB7182249127115749127115955ZFP36222621193989960339900002
BF969613PSMB71224809127115746127119158MARCH14684924164585083164585107
DW438983PSMB7171879127171672127171842PDS5B187243133321428533214341

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 # sample1             1  
GAIN (# sample)1             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=7)
Stat. for Synonymous SNVs
(# total SNVs=2)
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
chr9:127115993-127115993p.?1
chr9:127177679-127177679p.P9L1
chr9:127119142-127119142p.N208S1
chr9:127177691-127177691p.S5*1
chr9:127167675-127167675p.G144G1
chr9:127174656-127174656p.R124W1
chr9:127174763-127174763p.G88V1
chr9:127176280-127176280p.G54V1
chr9:127177161-127177161p.V39A1
chr9:127177167-127177167p.P37L1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample      1 1  11   1112
# mutation      1 1  11   1112
nonsynonymous SNV      1 1       1 11
synonymous SNV           11    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
chr9:127167675p.G54V1
chr9:127176280p.C19C1
chr9:127177648p.G12E1
chr9:127177670p.V11D1
chr9:127177673p.P9L1
chr9:127177679p.S5S1
chr9:127177690p.T270T1
chr9:127115901p.N208S1
chr9:127119142p.G144G1

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 PSMB7 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 PSMB7

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

ARPC5L,COX6B1,DPM2,EDF1,LSM4,MED27,NTMT1,
NDUFA8,PSMB7,PSMC1,PTGES2,RABEPK,RPL35,SEC61B,
SNRPF,SSNA1,SURF2,TXN,WDR34,ZDHHC12,ZMYND19
CCT7,CHCHD2,COPS6,COX4I1,DCTN3,EIF3I,EIF3K,
GRHPR,LOC440957,MRPL11,MRPL20,MRPL43,MRPL51,MRPS18A,
NDUFA11,PARK7,POLR2I,PSMB7,STOML2,TXN2,ZNF511

ARPC5L,CKS2,DPM2,EDF1,MED27,NTMT1,MRPS2,
NDUFA8,PMPCA,PSMB1,PSMB7,PTTG1,RPL35,RPL7A,
SEC61B,SSNA1,TMEM203,TRUB2,TXN,URM1,ZMYND19
TMEM258,EMC7,DAD1,LSM3,MRPL52,NDUFA7,NDUFB4,
NEDD8,OSGEP,POLR2L,PSMA1,PSMA2,PSMA5,PSMA7,
PSMB1,PSMB3,PSMB4,PSMB7,PSMD13,PSMD8,RBX1
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 PSMB7
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, 7experimentalN-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB08515proteasome (prosome, macropain) subunit, beta type, 7experimental(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, 7approved; nutraceuticalAdenosine triphosphate


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Cross referenced IDs for PSMB7
* 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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