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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) |
Cancer Description | |
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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA |
Others | |
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. |
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 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 |
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=15) | (# total SNVs=1) |
(# total SNVs=1) | (# 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 |
chr15:78834927-78834927 | p.R50H | 2 |
chr15:78836605-78836605 | p.Q95E | 1 |
chr15:78839018-78839018 | p.V203V | 1 |
chr15:78837210-78837210 | p.? | 1 |
chr15:78841153-78841153 | p.R218T | 1 |
chr15:78834828-78834828 | p.R17L | 1 |
chr15:78837236-78837236 | p.I105V | 1 |
chr15:78841185-78841185 | p.K229E | 1 |
chr15:78834913-78834913 | p.L45L | 1 |
chr15:78837238-78837238 | p.I105M | 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 |   |   |   |   | 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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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 |
chr15:78838990 | p.K158E,PSMA4 | 1 |
chr15:78839018 | p.R178C,PSMA4 | 1 |
chr15:78834894 | p.R178H,PSMA4 | 1 |
chr15:78841185 | p.A39V,PSMA4 | 1 |
chr15:78834926 | p.R50S,PSMA4 | 1 |
chr15:78841245 | p.D57A,PSMA4 | 1 |
chr15:78834948 | p.V59A,PSMA4 | 1 |
chr15:78841246 | p.I8L,PSMA4 | 1 |
chr15:78834954 | p.I34M,PSMA4 | 1 |
chr15:78836557 | p.A42V,PSMA4 | 1 |
Other DBs for Point Mutations |
Copy Number for PSMA4 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 PSMA4 |
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 |
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 | ||||
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 |
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 PSMA4 |
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, 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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