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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PSMA4 |
Basic gene info. | Gene symbol | PSMA4 |
Gene name | proteasome (prosome, macropain) subunit, alpha type, 4 | |
Synonyms | HC9|HsT17706|PSC9 | |
Cytomap | UCSC genome browser: 15q25.1 | |
Genomic location | chr15 :78832746-78841563 | |
Type of gene | protein-coding | |
RefGenes | NM_001102667.1, NM_001102668.1,NM_002789.4, | |
Ensembl id | ENSG00000041357 | |
Description | macropain subunit C9multicatalytic endopeptidase complex subunit C9proteasome component C9proteasome subunit HC9proteasome subunit Lproteasome subunit alpha type-4 | |
Modification date | 20141207 | |
dbXrefs | MIM : 176846 | |
HGNC : HGNC | ||
Ensembl : ENSG00000041357 | ||
HPRD : 10168 | ||
Vega : OTTHUMG00000143859 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PSMA4 | |
BioGPS: 5685 | ||
Gene Expression Atlas: ENSG00000041357 | ||
The Human Protein Atlas: ENSG00000041357 | ||
Pathway | NCI Pathway Interaction Database: PSMA4 | |
KEGG: PSMA4 | ||
REACTOME: PSMA4 | ||
ConsensusPathDB | ||
Pathway Commons: PSMA4 | ||
Metabolism | MetaCyc: PSMA4 | |
HUMANCyc: PSMA4 | ||
Regulation | Ensembl's Regulation: ENSG00000041357 | |
miRBase: chr15 :78,832,746-78,841,563 | ||
TargetScan: NM_001102667 | ||
cisRED: ENSG00000041357 | ||
Context | iHOP: PSMA4 | |
cancer metabolism search in PubMed: PSMA4 | ||
UCL Cancer Institute: PSMA4 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PSMA4(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PSMA4 |
Familial Cancer Database: PSMA4 |
* 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: PSMA4 |
MedGen: PSMA4 (Human Medical Genetics with Condition) | |
ClinVar: PSMA4 | |
Phenotype | MGI: PSMA4 (International Mouse Phenotyping Consortium) |
PhenomicDB: PSMA4 |
Mutations for PSMA4 |
* 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 PSMA4 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 |
BU190440 | PSMA4 | 2 | 311 | 15 | 78841212 | 78841523 | PSAP | 304 | 820 | 10 | 73578373 | 73579633 | |
AW149658 | RAB31 | 2 | 276 | 18 | 9862275 | 9862549 | PSMA4 | 267 | 622 | 15 | 78841164 | 78841518 |
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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=15) | (# total SNVs=1) |
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(# total SNVs=1) | (# 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 |
chr15:78834927-78834927 | p.R50H | 2 |
chr15:78834948-78834948 | p.D57A | 1 |
chr15:78837982-78837982 | p.R128H | 1 |
chr15:78841258-78841258 | p.E253G | 1 |
chr15:78834954-78834954 | p.V59A | 1 |
chr15:78837990-78837990 | p.G131C | 1 |
chr15:78834977-78834977 | p.K67E | 1 |
chr15:78838104-78838104 | p.A169S | 1 |
chr15:78834992-78834992 | p.? | 1 |
chr15:78838948-78838950 | p.E181delE | 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 |   |   |   | 2 |   |   |   |   | 2 |   |   | 2 | 1 | 1 |   |   |   | 2 |   | 2 |
# mutation |   |   |   | 2 |   |   |   |   | 2 |   |   | 2 | 1 | 1 |   |   |   | 3 |   | 2 |
nonsynonymous SNV |   |   |   | 1 |   |   |   |   | 2 |   |   | 2 | 1 | 1 |   |   |   | 3 |   | 2 |
synonymous SNV |   |   |   | 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 |
chr15:78836557 | p.I34M,PSMA4 | 1 |
chr15:78837238 | p.A42V,PSMA4 | 1 |
chr15:78837261 | p.G60C,PSMA4 | 1 |
chr15:78837990 | p.A98S,PSMA4 | 1 |
chr15:78838104 | p.I123S,PSMA4 | 1 |
chr15:78838990 | p.V132V,PSMA4 | 1 |
chr15:78839018 | p.K158E,PSMA4 | 1 |
chr15:78834894 | p.R178C,PSMA4 | 1 |
chr15:78841185 | p.R178H,PSMA4 | 1 |
chr15:78834926 | p.A39V,PSMA4 | 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 PSMA4 |
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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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HYKK,BOLA3,COX5A,FAM103A1,FBXO22,FBXO22-AS1,IDH3A, IMP3,MORF4L1,MRPS11,MTHFS,PSMA3,PSMA4,PSMA5, PSMD14,RCN2,SNRPA1,SNRPG,SNUPN,TIPIN,WDR61 | ARPC2,CMC2,C20orf24,CCDC53,CDC123,EIF2S2,GTF3C6, LSM3,MRPL47,NOP10,POMP,PSMA1,PSMA3,PSMA4, PSMA5,PSMA6,RBX1,SNRPG,TOMM5,TTC1,ZBTB8OS | ||||
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EMC7,CCNB2,DUT,ERH,FAM96A,FBXO22,KIAA0101, MRPL46,MRPS11,MTHFS,NOP10,OIP5,PSMA3,PSMA4, PSMA5,PSMA6,RAB11A,SEC11A,SRSF3,TIPIN,WDR61 | C1GALT1C1,DYNLT1,EIF5A,EIF5AL1,ERH,GOLT1B,NMI, POMP,PPA1,PSMA1,PSMA2,PSMA3,PSMA4,PSMA5, PSMA6,PSMA7,PSMB1,PSMB4,RASL11A,SARNP,TMSB10 |
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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 PSMA4 |
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DB Category | DB Name | DB's ID and Url link |
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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, 4 | experimental | N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE | ![]() | ![]() |
DB08515 | proteasome (prosome, macropain) subunit, alpha 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, alpha type, 4 | approved; nutraceutical | Adenosine triphosphate | ![]() | ![]() |
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Cross referenced IDs for PSMA4 |
* 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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