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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PSMA6 |
Basic gene info. | Gene symbol | PSMA6 |
Gene name | proteasome (prosome, macropain) subunit, alpha type, 6 | |
Synonyms | IOTA|PROS27|p27K | |
Cytomap | UCSC genome browser: 14q13 | |
Genomic location | chr14 :35761573-35786682 | |
Type of gene | protein-coding | |
RefGenes | NM_001282232.1, NM_001282233.1,NM_001282234.1,NM_002791.2,NR_104110.1, | |
Ensembl id | ENSG00000100902 | |
Description | 27 kDa prosomal proteinPROS-27macropain iota chainmacropain subunit iotamulticatalytic endopeptidase complex iota chainprosomal P27K proteinproteasome iota chainproteasome subunit alpha type-6proteasome subunit iota | |
Modification date | 20141207 | |
dbXrefs | MIM : 602855 | |
HGNC : HGNC | ||
Ensembl : ENSG00000100902 | ||
HPRD : 04171 | ||
Vega : OTTHUMG00000140221 | ||
Protein | UniProt: P60900 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PSMA6 | |
BioGPS: 5687 | ||
Gene Expression Atlas: ENSG00000100902 | ||
The Human Protein Atlas: ENSG00000100902 | ||
Pathway | NCI Pathway Interaction Database: PSMA6 | |
KEGG: PSMA6 | ||
REACTOME: PSMA6 | ||
ConsensusPathDB | ||
Pathway Commons: PSMA6 | ||
Metabolism | MetaCyc: PSMA6 | |
HUMANCyc: PSMA6 | ||
Regulation | Ensembl's Regulation: ENSG00000100902 | |
miRBase: chr14 :35,761,573-35,786,682 | ||
TargetScan: NM_001282232 | ||
cisRED: ENSG00000100902 | ||
Context | iHOP: PSMA6 | |
cancer metabolism search in PubMed: PSMA6 | ||
UCL Cancer Institute: PSMA6 | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of PSMA6 in cancer cell metabolism | 1. Jastrzebski K, Hannan KM, House CM, Hung SS, Pearson RB, et al. (2011) A phospho-proteomic screen identifies novel S6K1 and mTORC1 substrates revealing additional complexity in the signaling network regulating cell growth. Cell Signal 23: 1338-1347. doi: 10.1016/j.cellsig.2011.03.016. go to article |
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Phenotypic Information for PSMA6(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PSMA6 |
Familial Cancer Database: PSMA6 |
* 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 | 602855; gene. |
Orphanet | |
Disease | KEGG Disease: PSMA6 |
MedGen: PSMA6 (Human Medical Genetics with Condition) | |
ClinVar: PSMA6 | |
Phenotype | MGI: PSMA6 (International Mouse Phenotyping Consortium) |
PhenomicDB: PSMA6 |
Mutations for PSMA6 |
* 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 PSMA6 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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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
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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Stat. for Non-Synonymous SNVs (# total SNVs=15) | (# total SNVs=1) |
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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 |
chr14:35761686-35761686 | p.S2P | 1 |
chr14:35778193-35778193 | p.G82A | 1 |
chr14:35782239-35782239 | p.D188H | 1 |
chr14:35761712-35761712 | p.D10E | 1 |
chr14:35778201-35778201 | p.A85S | 1 |
chr14:35782253-35782253 | p.E192E | 1 |
chr14:35761737-35761737 | p.E19Q | 1 |
chr14:35780014-35780014 | p.E108Q | 1 |
chr14:35783559-35783559 | p.? | 1 |
chr14:35761756-35761756 | p.V25A | 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 | 1 | 1 |   |   |   | 1 |   | 2 |   |   | 4 | 1 |   |   | 1 | 2 | 4 | 1 | 1 |
# mutation | 1 | 1 | 1 |   |   |   | 1 |   | 2 |   |   | 5 | 1 |   |   | 1 | 2 | 5 | 1 | 1 |
nonsynonymous SNV | 1 | 1 | 1 |   |   |   | 1 |   | 2 |   |   | 4 | 1 |   |   |   | 2 | 5 | 1 | 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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* 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 |
chr14:35761686 | p.D109H,PSMA6 | 1 |
chr14:35780014 | p.D10E | 1 |
chr14:35761712 | p.E113E,PSMA6 | 1 |
chr14:35780027 | p.P18P | 1 |
chr14:35761736 | p.D157H,PSMA6 | 1 |
chr14:35780041 | p.V25A | 1 |
chr14:35761756 | p.A162V,PSMA6 | 1 |
chr14:35780051 | p.I13L,PSMA6 | 1 |
chr14:35777217 | p.E165Q,PSMA6 | 1 |
chr14:35782140 | p.G17S,PSMA6 | 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 PSMA6 |
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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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BAZ1A,DTD2,C20orf24,DAD1,DKFZp686A1627,EAPP,FAM177A1, FKBP3,KIAA0391,NEDD8,PIGU,LRR1,PPP2R3C,PSMA3, PSMA6,PSME2,RBMY1E,SCAF11___GEMIN2___ZEB2,SNX6,SRP54,TACO1 | ATP5E,ATP5L,SLIRP,C14orf2,EIF2S2,ENY2,GTF3A, LAMTOR5,LSM3,NDUFB1,POMP,PSMA1,PSMA2,PSMA3, PSMA6,PSMB1,PSMC1,PSMD6,TOMM5,TTC1,UBE2F | ||||
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ASNA1,C14orf119,C14orf142,C14orf2,CNIH1,DAD1,EIF2S1, ERH,ISCA2,MRPL52,MRPL54,NDUFB1,NEDD8,PHF5A, PSMA3,PSMA6,PSMB5,PSMC6,PSME1,PSME2,ZNF410 | EMC7,CKLF,DYNLT1,FAM49B,LSM1,NDUFV2,PGK1, POMP,PSMA1,PSMA2,PSMA3,PSMA4,PSMA5,PSMA6, PSMA7,PSMB1,PSMB3,PSMB4,PSMD13,RBX1,UFD1L |
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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 PSMA6 |
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DB Category | DB Name | DB's ID and Url link |
Chemistry | ChEMBL | CHEMBL2364701; -. |
Organism-specific databases | PharmGKB | PA33880; -. |
Organism-specific databases | CTD | 5687; -. |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB07475 | proteasome (prosome, macropain) subunit, alpha type, 6 | experimental | N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE | ![]() | ![]() |
DB08515 | proteasome (prosome, macropain) subunit, alpha type, 6 | 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, alpha type, 6 | approved; nutraceutical | Adenosine triphosphate | ![]() | ![]() |
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Cross referenced IDs for PSMA6 |
* 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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