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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PSMD4 |
Basic gene info. | Gene symbol | PSMD4 |
Gene name | proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 | |
Synonyms | AF|AF-1|ASF|MCB1|Rpn10|S5A|pUB-R5 | |
Cytomap | UCSC genome browser: 1q21.3 | |
Genomic location | chr1 :151227196-151239954 | |
Type of gene | protein-coding | |
RefGenes | NM_002810.2, NM_153822.2, | |
Ensembl id | ENSG00000159352 | |
Description | 26S proteasome non-ATPase regulatory subunit 426S proteasome regulatory subunit S5AS5a/antisecretory factor proteinangiocidinantisecretory factor 1multiubiquitin chain-binding protein | |
Modification date | 20141207 | |
dbXrefs | MIM : 601648 | |
HGNC : HGNC | ||
Ensembl : ENSG00000159352 | ||
HPRD : 03386 | ||
Vega : OTTHUMG00000012349 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PSMD4 | |
BioGPS: 5710 | ||
Gene Expression Atlas: ENSG00000159352 | ||
The Human Protein Atlas: ENSG00000159352 | ||
Pathway | NCI Pathway Interaction Database: PSMD4 | |
KEGG: PSMD4 | ||
REACTOME: PSMD4 | ||
ConsensusPathDB | ||
Pathway Commons: PSMD4 | ||
Metabolism | MetaCyc: PSMD4 | |
HUMANCyc: PSMD4 | ||
Regulation | Ensembl's Regulation: ENSG00000159352 | |
miRBase: chr1 :151,227,196-151,239,954 | ||
TargetScan: NM_002810 | ||
cisRED: ENSG00000159352 | ||
Context | iHOP: PSMD4 | |
cancer metabolism search in PubMed: PSMD4 | ||
UCL Cancer Institute: PSMD4 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PSMD4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PSMD4 |
Familial Cancer Database: PSMD4 |
* This gene is included in those cancer gene databases. |
. | ||||||||||||||||||||
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: PSMD4 |
MedGen: PSMD4 (Human Medical Genetics with Condition) | |
ClinVar: PSMD4 | |
Phenotype | MGI: PSMD4 (International Mouse Phenotyping Consortium) |
PhenomicDB: PSMD4 |
Mutations for PSMD4 |
* 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 |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
pancreas | PSMD4 | chr1 | 151236464 | 151236484 | PI4KB | chr1 | 151295275 | 151295295 |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PSMD4 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 |
BU590293 | RPS9 | 1 | 325 | 19 | 54705447 | 54711372 | PSMD4 | 312 | 506 | 1 | 151239761 | 151239955 | |
BU538390 | C20orf27 | 1 | 335 | 20 | 3734588 | 3735159 | PSMD4 | 335 | 670 | 1 | 151237348 | 151238086 | |
U51007 | IQGAP1 | 7 | 128 | 15 | 91045344 | 91045467 | PSMD4 | 119 | 1323 | 1 | 151227233 | 151239865 |
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=24) | (# total SNVs=4) |
(# 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 |
chr1:151234659-151234659 | p.R17W | 2 |
chr1:151237660-151237660 | p.R130C | 1 |
chr1:151238534-151238534 | p.R237W | 1 |
chr1:151227268-151227268 | p.E4Q | 1 |
chr1:151239784-151239784 | p.G367S | 1 |
chr1:151237667-151237667 | p.K132R | 1 |
chr1:151238792-151238792 | p.D258N | 1 |
chr1:151234658-151234658 | p.M16I | 1 |
chr1:151239791-151239791 | p.K369R | 1 |
chr1:151237890-151237890 | p.L153L | 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 | 2 |   | 3 | 1 |   | 3 |   | 2 |   |   | 5 | 1 |   |   |   | 2 | 2 |   | 3 |
# mutation | 1 | 2 |   | 4 | 1 |   | 3 |   | 2 |   |   | 5 | 1 |   |   |   | 2 | 2 |   | 4 |
nonsynonymous SNV | 1 | 2 |   | 2 | 1 |   | 1 |   | 2 |   |   | 1 | 1 |   |   |   | 2 | 1 |   | 4 |
synonymous SNV |   |   |   | 2 |   |   | 2 |   |   |   |   | 4 |   |   |   |   |   | 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 |
chr1:151234661 | p.R17R | 2 |
chr1:151237667 | p.T88M | 1 |
chr1:151238867 | p.E283Q | 1 |
chr1:151227268 | p.R91R | 1 |
chr1:151237890 | p.D309Y | 1 |
chr1:151239025 | p.R108C | 1 |
chr1:151234658 | p.P332P | 1 |
chr1:151237896 | p.R130C | 1 |
chr1:151239681 | p.P347P | 1 |
chr1:151234659 | p.L131L | 1 |
Other DBs for Point Mutations |
Copy Number for PSMD4 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 PSMD4 |
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 |
BOLA1,C1orf35,CRTC2,DPM3,HAX1,JTB,MRPL24, MRPL55,MRPL9,MRPS21,MTX1,PFDN2,PIPSL,PMF1, PSMB4,PSMD4,RAB13,LAMTOR2,SCNM1,SF3B4,VPS72 | AKT1S1,BLOC1S1,BABAM1,RTFDC1,COPS6,FIS1,GRHPR, MAF1,MRPL16,MRPL24,MRPL2,MRPS11,NDUFA13,NDUFB7, NDUFS6,PARK7,PPP1R7,PSMB6,PSMC3,PSMD4,STUB1 | ||||
C1orf35,CCT3,DAP3,HAX1,JTB,KRTCAP2,MRPL24, MRPL55,MRPL9,MTX1,PFDN2,PMVK,PPOX,PSMB4, PSMD4,PYCR2,LAMTOR2,SCAMP3,SCNM1,SNRPE,VPS72 | C11orf73,COPRS,BRK1,COPS6,CREB3,DPCD,DRAP1, MANBAL,MEA1,MPV17,NUBP1,PARK7,PFDN1,PSMB6, PSMC3,PSMD4,RANGRF,SNAPIN,SSSCA1,TRMT112,UROD |
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 PSMD4 |
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 |
DB00171 | proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 | approved; nutraceutical | Adenosine triphosphate |
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Cross referenced IDs for PSMD4 |
* 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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