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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PSMA1 |
Basic gene info. | Gene symbol | PSMA1 |
Gene name | proteasome (prosome, macropain) subunit, alpha type, 1 | |
Synonyms | HC2|HEL-S-275|NU|PROS30 | |
Cytomap | UCSC genome browser: 11p15.1 | |
Genomic location | chr11 :14526421-14541991 | |
Type of gene | protein-coding | |
RefGenes | NM_001143937.1, NM_002786.3,NM_148976.2, | |
Ensembl id | ENSG00000129084 | |
Description | 30 kDa prosomal proteinPROS-30epididymis secretory protein Li 275macropain subunit C2macropain subunit numulticatalytic endopeptidase complex subunit C2proteasome component C2proteasome nu chainproteasome subunit alpha type-1proteasome subunit nu | |
Modification date | 20141207 | |
dbXrefs | MIM : 602854 | |
HGNC : HGNC | ||
Ensembl : ENSG00000129084 | ||
HPRD : 04170 | ||
Vega : OTTHUMG00000165825 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PSMA1 | |
BioGPS: 5682 | ||
Gene Expression Atlas: ENSG00000129084 | ||
The Human Protein Atlas: ENSG00000129084 | ||
Pathway | NCI Pathway Interaction Database: PSMA1 | |
KEGG: PSMA1 | ||
REACTOME: PSMA1 | ||
ConsensusPathDB | ||
Pathway Commons: PSMA1 | ||
Metabolism | MetaCyc: PSMA1 | |
HUMANCyc: PSMA1 | ||
Regulation | Ensembl's Regulation: ENSG00000129084 | |
miRBase: chr11 :14,526,421-14,541,991 | ||
TargetScan: NM_001143937 | ||
cisRED: ENSG00000129084 | ||
Context | iHOP: PSMA1 | |
cancer metabolism search in PubMed: PSMA1 | ||
UCL Cancer Institute: PSMA1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PSMA1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PSMA1 |
Familial Cancer Database: PSMA1 |
* 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: PSMA1 |
MedGen: PSMA1 (Human Medical Genetics with Condition) | |
ClinVar: PSMA1 | |
Phenotype | MGI: PSMA1 (International Mouse Phenotyping Consortium) |
PhenomicDB: PSMA1 |
Mutations for PSMA1 |
* 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 PSMA1 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 |
BP386202 | SSR1 | 1 | 313 | 6 | 7281604 | 7281915 | PSMA1 | 314 | 500 | 11 | 14526424 | 14526610 | |
DA097339 | PSMA1 | 1 | 121 | 11 | 14561925 | 14562045 | PKP4 | 119 | 562 | 2 | 159433781 | 159477909 |
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=1) | (# total SNVs=0) |
(# 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 |
chr11:14526779-14526779 | p.D251Y | 1 |
chr11:14529241-14529241 | p.F232F | 1 |
chr11:14539218-14539218 | p.A75V | 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 | 1 |   | 2 |   |   | 2 |   | 1 |   |   | 2 |   |   |   | 1 | 4 | 2 |   | 3 |
# mutation | 1 | 1 |   | 2 |   |   | 2 |   | 1 |   |   | 2 |   |   |   | 1 | 4 | 2 |   | 3 |
nonsynonymous SNV | 1 | 1 |   | 1 |   |   | 2 |   | 1 |   |   | 2 |   |   |   | 1 | 4 | 2 |   | 1 |
synonymous SNV |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 2 |
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 |
chr11:14535995 | p.F99F,PSMA1 | 2 |
chr11:14539218 | p.A75V,PSMA1 | 2 |
chr11:14535392 | p.A121S | 1 |
chr11:14526746 | p.Q60H,PSMA1 | 1 |
chr11:14535931 | p.T42T,PSMA1 | 1 |
chr11:14526749 | p.E262K,PSMA1 | 1 |
chr11:14526751 | p.Q31R,PSMA1 | 1 |
chr11:14526784 | p.M261V,PSMA1 | 1 |
chr11:14539262 | p.N4S,PSMA1 | 1 |
chr11:14529245 | p.P260L,PSMA1 | 1 |
Other DBs for Point Mutations |
Copy Number for PSMA1 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 PSMA1 |
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 |
BTBD10,C11orf58,CCNB1,COPB1,GTF2H1,HTATIP2,KIF18A, LDHA,MTCH2,PRMT3,PSMA1,PSMA2,PSMA3,PSMD14, RRAS2,SAAL1,TALDO1,TSG101,TXNL1,VPS29,ZDHHC13 | C20orf24,EIF2S2,GNG5,LSM3,MRPL47,POMP,PSMA1, PSMA2,PSMA3,PSMA4,PSMA6,PSMD6,RHEB,SUMO1, THOC7,TOMM5,TTC1,TXNL1,UBE2D2,UBE2V1,YWHAE | ||||
ATP5L,C11orf58,C11orf73,CCDC59,DCUN1D5,EIF3M,GLRX3, LSM3,MRPS23,NDUFS3,POLR2G,PSMA1,PSMA2,PSMB1, PSMD13,PSMD14,PTPMT1,SRSF3,SNRPG,TIMM8B,TMEM126A | SLIRP,EMC7,DYNLT1,PGK1,POMP,PPA1,PSMA1, PSMA2,PSMA3,PSMA4,PSMA5,PSMA6,PSMA7,PSMB1, PSMC2,PSMC6,PSMD13,PSMD14,RBX1,SNRPG,UFD1L |
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 PSMA1 |
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, alpha type, 1 | experimental | N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE | ||
DB08515 | proteasome (prosome, macropain) subunit, alpha type, 1 | 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, 1 | approved; nutraceutical | Adenosine triphosphate |
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Cross referenced IDs for PSMA1 |
* 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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