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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PSMB9 |
Basic gene info. | Gene symbol | PSMB9 |
Gene name | proteasome (prosome, macropain) subunit, beta type, 9 | |
Synonyms | LMP2|PSMB6i|RING12|beta1i | |
Cytomap | UCSC genome browser: 6p21.3 | |
Genomic location | chr6 :32821937-32827628 | |
Type of gene | protein-coding | |
RefGenes | NM_002800.4, NM_148954.2, | |
Ensembl id | ENSG00000240065 | |
Description | large multifunctional peptidase 2low molecular mass protein 2macropain chain 7multicatalytic endopeptidase complex chain 7proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional peptidase 2)proteasome catalytic subunit 1iproteas | |
Modification date | 20141207 | |
dbXrefs | MIM : 177045 | |
HGNC : HGNC | ||
HPRD : 01514 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PSMB9 | |
BioGPS: 5698 | ||
Gene Expression Atlas: ENSG00000240065 | ||
The Human Protein Atlas: ENSG00000240065 | ||
Pathway | NCI Pathway Interaction Database: PSMB9 | |
KEGG: PSMB9 | ||
REACTOME: PSMB9 | ||
ConsensusPathDB | ||
Pathway Commons: PSMB9 | ||
Metabolism | MetaCyc: PSMB9 | |
HUMANCyc: PSMB9 | ||
Regulation | Ensembl's Regulation: ENSG00000240065 | |
miRBase: chr6 :32,821,937-32,827,628 | ||
TargetScan: NM_002800 | ||
cisRED: ENSG00000240065 | ||
Context | iHOP: PSMB9 | |
cancer metabolism search in PubMed: PSMB9 | ||
UCL Cancer Institute: PSMB9 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PSMB9(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PSMB9 |
Familial Cancer Database: PSMB9 |
* 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/ |
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REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: PSMB9 |
MedGen: PSMB9 (Human Medical Genetics with Condition) | |
ClinVar: PSMB9 | |
Phenotype | MGI: PSMB9 (International Mouse Phenotyping Consortium) |
PhenomicDB: PSMB9 |
Mutations for PSMB9 |
* 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PSMB9 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 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=11) | (# total SNVs=3) |
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(# total SNVs=0) | (# total SNVs=0) |
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* 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 |
chr6:32825140-32825140 | p.D77N | 2 |
chr6:32827290-32827290 | p.P214L | 2 |
chr6:32825852-32825852 | p.R111* | 2 |
chr6:32825086-32825086 | p.E59K | 1 |
chr6:32827219-32827219 | p.G190G | 1 |
chr6:32827225-32827225 | p.V192V | 1 |
chr6:32825782-32825782 | p.G87G | 1 |
chr6:32825836-32825836 | p.N105K | 1 |
chr6:32827297-32827297 | p.F216L | 1 |
chr6:32825904-32825904 | p.G128E | 1 |
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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 |   |   | 4 |   |   |   |   |   |   |   | 2 | 1 | 1 |   |   | 1 | 2 |   | 1 |
# mutation | 1 |   |   | 3 |   |   |   |   |   |   |   | 3 | 1 | 1 |   |   | 1 | 2 |   | 1 |
nonsynonymous SNV | 1 |   |   | 3 |   |   |   |   |   |   |   | 1 | 1 | 1 |   |   |   | 1 |   | 1 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   | 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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* 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 |
chr6:32825078 | p.P56L | 2 |
chr6:32825140 | p.D77N | 1 |
chr6:32825836 | p.N105K | 1 |
chr6:32825904 | p.G128E | 1 |
chr6:32826184 | p.A145V | 1 |
chr6:32827190 | p.L181V | 1 |
chr6:32827217 | p.G190W | 1 |
chr6:32827218 | p.G190V | 1 |
chr6:32827219 | p.G190G | 1 |
chr6:32823969 | p.V192V | 1 |
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* 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. |
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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 PSMB9 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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APOL1,APOL3,B2M,CD74,ETV7,HCP5,HLA-A, HLA-B,HLA-C,HLA-DMA,HLA-E,HLA-F,HLA-H,IL18BP, IRF1,NLRC5,PSMB8,PSMB9,TAP1,TAP2,TAPBP | ABI3,APOL1,CARD16,CD74,CST7,GZMA,GZMB, HLA-A,HLA-B,HLA-DPB1,HLA-DRA,HLA-F,IFITM1,IFITM3, IL18BP,NKG7,PSMB8,PSMB9,TAP1,TMEM173,UBE2L6 |
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BATF2,CD74,ETV7,FBXO6,GBP1,HCP5,HLA-C, HLA-DMA,HLA-E,HLA-F,IL15RA,IRF1,PSMB10,PSMB8, PSMB9,PSME1,PSME2,RARRES3,STAT1,TAP1,UBE2L6 | APOL2,BATF2,CXCL9,EPSTI1,ETV7,FAM26F,GBP1, GBP4,GBP5,IFI35,IRF1,PARP9,PSMB10,PSMB9, PSME1,PSME2,RARRES3,STAT1,TAP1,TRIM21,UBE2L6 |
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* 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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Pharmacological Information for PSMB9 |
There's no related Drug. |
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Cross referenced IDs for PSMB9 |
* 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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