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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PSMB4 |
Basic gene info. | Gene symbol | PSMB4 |
Gene name | proteasome (prosome, macropain) subunit, beta type, 4 | |
Synonyms | HN3|HsN3|PROS-26|PROS26 | |
Cytomap | UCSC genome browser: 1q21 | |
Genomic location | chr1 :151372040-151374412 | |
Type of gene | protein-coding | |
RefGenes | NM_002796.2, | |
Ensembl id | ENSG00000159377 | |
Description | 26 kDa prosomal proteinhsBPROS26macropain beta chainmulticatalytic endopeptidase complex beta chainproteasome beta chainproteasome chain 3proteasome subunit HsN3proteasome subunit beta type-4proteasome subunit, beta type, 4 | |
Modification date | 20141207 | |
dbXrefs | MIM : 602177 | |
HGNC : HGNC | ||
Ensembl : ENSG00000159377 | ||
HPRD : 03710 | ||
Vega : OTTHUMG00000012494 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PSMB4 | |
BioGPS: 5692 | ||
Gene Expression Atlas: ENSG00000159377 | ||
The Human Protein Atlas: ENSG00000159377 | ||
Pathway | NCI Pathway Interaction Database: PSMB4 | |
KEGG: PSMB4 | ||
REACTOME: PSMB4 | ||
ConsensusPathDB | ||
Pathway Commons: PSMB4 | ||
Metabolism | MetaCyc: PSMB4 | |
HUMANCyc: PSMB4 | ||
Regulation | Ensembl's Regulation: ENSG00000159377 | |
miRBase: chr1 :151,372,040-151,374,412 | ||
TargetScan: NM_002796 | ||
cisRED: ENSG00000159377 | ||
Context | iHOP: PSMB4 | |
cancer metabolism search in PubMed: PSMB4 | ||
UCL Cancer Institute: PSMB4 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PSMB4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PSMB4 |
Familial Cancer Database: PSMB4 |
* This gene is included in those cancer gene databases. |
. | ||||||||||||||||||||
Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PSMB4 |
MedGen: PSMB4 (Human Medical Genetics with Condition) | |
ClinVar: PSMB4 | |
Phenotype | MGI: PSMB4 (International Mouse Phenotyping Consortium) |
PhenomicDB: PSMB4 |
Mutations for PSMB4 |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PSMB4 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
CB854321 | PSMB4 | 1 | 59 | 1 | 151373238 | 151373296 | PSMB4 | 54 | 303 | 1 | 151373277 | 151374105 | |
BE179662 | PSMB4 | 11 | 72 | 1 | 151374318 | 151374379 | IGFN1 | 62 | 169 | 1 | 201178364 | 201178471 |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=12) | (# total SNVs=10) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr1:151372138-151372138 | p.P25P | 2 |
chr1:151373784-151373784 | p.R216C | 1 |
chr1:151372168-151372168 | p.A35A | 1 |
chr1:151372650-151372650 | p.L112I | 1 |
chr1:151374025-151374025 | p.I234T | 1 |
chr1:151372187-151372187 | p.P42A | 1 |
chr1:151372945-151372945 | p.G125G | 1 |
chr1:151374045-151374045 | p.G241S | 1 |
chr1:151372469-151372469 | p.V51V | 1 |
chr1:151372951-151372951 | p.S127S | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 |   |   | 3 |   |   | 1 |   |   | 1 |   | 2 | 3 | 3 |   |   | 2 | 6 |   | 3 |
# mutation | 1 |   |   | 3 |   |   | 1 |   |   | 1 |   | 4 | 3 | 3 |   |   | 2 | 6 |   | 3 |
nonsynonymous SNV | 1 |   |   |   |   |   | 1 |   |   |   |   | 3 | 2 | 2 |   |   | 1 | 3 |   | 2 |
synonymous SNV |   |   |   | 3 |   |   |   |   |   | 1 |   | 1 | 1 | 1 |   |   | 1 | 3 |   | 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr1:151372480 | p.A35A | 1 |
chr1:151373032 | p.G168C | 1 |
chr1:151372509 | p.A37A | 1 |
chr1:151373047 | p.A176A | 1 |
chr1:151372573 | p.T54T | 1 |
chr1:151373247 | p.A183T | 1 |
chr1:151372581 | p.S55L | 1 |
chr1:151373273 | p.A183V | 1 |
chr1:151372078 | p.V65L | 1 |
chr1:151372582 | p.R211S | 1 |
Other DBs for Point Mutations |
Copy Number for PSMB4 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 PSMB4 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
BOLA1,COA6,CRTC2,FAM71D,FLAD1,HAX1,JMJD4, JTB,KRTCAP2,MRPL9,MRPS21,PFDN2,PIPSL,PSMB4, PSMD4,RRP1,S100A11,SCNM1,SF3B4,UCK2,VPS72 | LAMTOR1,C17orf49,C19orf53,COPS6,MRPL20,MRPL43,NDUFA11, NENF,OAZ1,PPP1R7,PSMB4,RANGRF,RNASEK,RNF181, SF3B5,SSU72,TAF10,TMEM219,TRAPPC2L,URM1,ZNHIT1 | ||||
APOA1BP,COA6,C1orf43,CACYBP,FLAD1,HAX1,JTB, KRTCAP2,MRPL24,MRPL55,MRPL9,MRPS14,MTX1,NDUFA13, NENF,PSMB4,PSMD4,LAMTOR2,SCNM1,SNRPE,VPS72 | IFT43,CKLF,DYNLT1,GUK1,NDUFA7,NDUFB4,OSGEP, PSENEN,PSMA2,PSMA5,PSMA6,PSMA7,PSMB1,PSMB3, PSMB4,PSMB7,PSMD13,PSMD8,RBX1,RNF181,SNX17 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for PSMB4 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB07475 | proteasome (prosome, macropain) subunit, beta type, 4 | experimental | N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE | ||
DB08515 | proteasome (prosome, macropain) subunit, beta type, 4 | experimental | (3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE | ||
DB00171 | proteasome (prosome, macropain) subunit, beta type, 4 | approved; nutraceutical | Adenosine triphosphate | ||
DB01151 | proteasome (prosome, macropain) subunit, beta type, 4 | approved | Desipramine | ||
DB00472 | proteasome (prosome, macropain) subunit, beta type, 4 | approved | Fluoxetine |
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Cross referenced IDs for PSMB4 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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