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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PSMB8 |
Basic gene info. | Gene symbol | PSMB8 |
Gene name | proteasome (prosome, macropain) subunit, beta type, 8 | |
Synonyms | ALDD|D6S216|D6S216E|JMP|LMP7|NKJO|PSMB5i|RING10 | |
Cytomap | UCSC genome browser: 6p21.3 | |
Genomic location | chr6_qbl_hap6 :4040600-4044819 | |
Type of gene | protein-coding | |
RefGenes | NM_004159.4, NM_148919.3, | |
Ensembl id | ENSG00000204264 | |
Description | large multifunctional peptidase 7low molecular mass protein 7low molecular weight protein 7macropain subunit C13multicatalytic endopeptidase complex subunit C13protease component C13proteasome (prosome, macropain) subunit, beta type, 8 (large multif | |
Modification date | 20141207 | |
dbXrefs | MIM : 177046 | |
HGNC : HGNC | ||
Ensembl : ENSG00000204264 | ||
HPRD : 01515 | ||
Vega : OTTHUMG00000031285 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PSMB8 | |
BioGPS: 5696 | ||
Gene Expression Atlas: ENSG00000204264 | ||
The Human Protein Atlas: ENSG00000204264 | ||
Pathway | NCI Pathway Interaction Database: PSMB8 | |
KEGG: PSMB8 | ||
REACTOME: PSMB8 | ||
ConsensusPathDB | ||
Pathway Commons: PSMB8 | ||
Metabolism | MetaCyc: PSMB8 | |
HUMANCyc: PSMB8 | ||
Regulation | Ensembl's Regulation: ENSG00000204264 | |
miRBase: chr6_qbl_hap6 :4,040,600-4,044,819 | ||
TargetScan: NM_004159 | ||
cisRED: ENSG00000204264 | ||
Context | iHOP: PSMB8 | |
cancer metabolism search in PubMed: PSMB8 | ||
UCL Cancer Institute: PSMB8 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PSMB8(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PSMB8 |
Familial Cancer Database: PSMB8 |
* This gene is included in those cancer gene databases. |
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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: PSMB8 |
MedGen: PSMB8 (Human Medical Genetics with Condition) | |
ClinVar: PSMB8 | |
Phenotype | MGI: PSMB8 (International Mouse Phenotyping Consortium) |
PhenomicDB: PSMB8 |
Mutations for PSMB8 |
* 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 PSMB8 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 |
AI280186 | SERPINF1 | 1 | 96 | 17 | 1680762 | 1680857 | PSMB8 | 82 | 472 | 6 | 4239280 | 4240152 |
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=19) | (# total SNVs=3) |
(# 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 |
chr6:32809494-32809494 | p.V182M | 3 |
chr6:32809404-32809404 | p.R212W | 3 |
chr6:32810002-32810002 | p.S145L | 2 |
chr6:32810470-32810470 | p.R125H | 1 |
chr6:32808759-32808759 | p.Q266* | 1 |
chr6:32809455-32809455 | p.S195fs*53 | 1 |
chr6:32810726-32810726 | p.S92S | 1 |
chr6:32808772-32808772 | p.S261R | 1 |
chr6:32809461-32809461 | p.M193V | 1 |
chr6:32810816-32810816 | p.Q62Q | 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 | 2 | 1 | 2 | 7 | 2 |   | 1 |   | 1 |   |   | 1 | 1 |   |   |   | 6 | 3 |   | 3 |
# mutation | 2 | 1 | 2 | 7 | 2 |   | 1 |   | 1 |   |   | 1 | 1 |   |   |   | 6 | 3 |   | 3 |
nonsynonymous SNV | 1 | 1 | 2 | 6 | 2 |   | 1 |   |   |   |   |   | 1 |   |   |   | 4 | 2 |   | 2 |
synonymous SNV | 1 |   |   | 1 |   |   |   |   | 1 |   |   | 1 |   |   |   |   | 2 | 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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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 |
chr6:32809404 | p.G54S,PSMB8 | 2 |
chr6:32810842 | p.R212W,PSMB8 | 2 |
chr6:32811685 | p.D259Y,PSMB8 | 1 |
chr6:32808747 | p.Q62Q,PSMB8 | 1 |
chr6:32809494 | p.V255V,PSMB8 | 1 |
chr6:32811701 | p.M247I,PSMB8 | 1 |
chr6:32808780 | p.L53M,PSMB8 | 1 |
chr6:32809961 | p.T232T,PSMB8 | 1 |
chr6:32811717 | p.E48K,PSMB8 | 1 |
chr6:32808790 | p.P30R | 1 |
Other DBs for Point Mutations |
Copy Number for PSMB8 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 PSMB8 |
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 |
APOL1,APOL2,APOL3,B2M,ETV7,HCG26,HCP5, HLA-A,HLA-B,HLA-C,HLA-E,HLA-F,HLA-H,PSMB10, PSMB8,PSMB9,PSME2,TAP1,TAP2,TAPBP,UBE2L6 | ABI3,BAX,CD7,CSK,ETV7,HLA-A,HLA-B, HLA-C,HLA-DPB1,HLA-F,PSMB10,PSMB8,PSMB9,PSME1, PSME2,RGS19,SH3BP1,TAP1,TAPBP,TRIM47,UBE2L6 |
BAK1,BATF2,ETV7,FBXO6,HCP5,HLA-B,HLA-C, HLA-E,HLA-F,IL15RA,IRF1,NMI,PARP9,PSMB10, PSMB8,PSMB9,PSME1,PSME2,RARRES3,TAP1,UBE2L6 | BATF2,CARD16,CASP1,EPSTI1,ETV7,FAM26F,FBXO6, IFI30,IFI35,IRF1,NMI,PSMB10,PSMB3,PSMB8, PSMB9,PSME1,RARRES3,RTP4,TAP1,TRIM21,UBE2L6 |
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 PSMB8 |
There's no related Drug. |
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Cross referenced IDs for PSMB8 |
* 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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