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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PSMD3 |
Basic gene info. | Gene symbol | PSMD3 |
Gene name | proteasome (prosome, macropain) 26S subunit, non-ATPase, 3 | |
Synonyms | P58|RPN3|S3|TSTA2 | |
Cytomap | UCSC genome browser: 17q21.1 | |
Genomic location | chr17 :38137059-38154212 | |
Type of gene | protein-coding | |
RefGenes | NM_002809.3, | |
Ensembl id | ENSG00000108344 | |
Description | 26S proteasome non-ATPase regulatory subunit 326S proteasome regulatory subunit RPN326S proteasome regulatory subunit S3proteasome subunit p58tissue specific transplantation antigen 2 | |
Modification date | 20141207 | |
dbXrefs | HGNC : HGNC | |
Ensembl : ENSG00000108344 | ||
HPRD : 10170 | ||
Vega : OTTHUMG00000133251 | ||
Protein | UniProt: O43242 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PSMD3 | |
BioGPS: 5709 | ||
Gene Expression Atlas: ENSG00000108344 | ||
The Human Protein Atlas: ENSG00000108344 | ||
Pathway | NCI Pathway Interaction Database: PSMD3 | |
KEGG: PSMD3 | ||
REACTOME: PSMD3 | ||
ConsensusPathDB | ||
Pathway Commons: PSMD3 | ||
Metabolism | MetaCyc: PSMD3 | |
HUMANCyc: PSMD3 | ||
Regulation | Ensembl's Regulation: ENSG00000108344 | |
miRBase: chr17 :38,137,059-38,154,212 | ||
TargetScan: NM_002809 | ||
cisRED: ENSG00000108344 | ||
Context | iHOP: PSMD3 | |
cancer metabolism search in PubMed: PSMD3 | ||
UCL Cancer Institute: PSMD3 | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
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Phenotypic Information for PSMD3(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PSMD3 |
Familial Cancer Database: PSMD3 |
* 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: PSMD3 |
MedGen: PSMD3 (Human Medical Genetics with Condition) | |
ClinVar: PSMD3 | |
Phenotype | MGI: PSMD3 (International Mouse Phenotyping Consortium) |
PhenomicDB: PSMD3 |
Mutations for PSMD3 |
* 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 | PSMD3 | chr17 | 38138356 | 38138376 | PSMD3 | chr17 | 38138736 | 38138756 |
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 PSMD3 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 |
BC001684 | PSMD3 | 9 | 1359 | 17 | 38137072 | 38151531 | PRELID1 | 1349 | 2256 | 5 | 176730830 | 176733662 | |
BQ361077 | MIB2 | 53 | 357 | 1 | 1561050 | 1561355 | PSMD3 | 355 | 595 | 17 | 38145990 | 38146394 | |
BM824189 | ASAP1 | 13 | 87 | 8 | 131124494 | 131124568 | PSMD3 | 82 | 165 | 17 | 38153778 | 38153861 | |
AW376286 | CHURC1 | 2 | 352 | 14 | 65406075 | 65406426 | PSMD3 | 352 | 478 | 17 | 38146010 | 38146136 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 2 |   |   | 2 |   |   | 1 |   |   |   |   |   |   |   | 2 |   |   | |||
GAIN (# sample) | 2 |   |   | 2 |   |   | 1 |   |   |   |   |   |   |   | 2 |   |   | |||
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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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=46) | (# total SNVs=10) |
(# 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 |
chr17:38151480-38151480 | p.G383V | 4 |
chr17:38140673-38140673 | p.A116V | 3 |
chr17:38151308-38151308 | p.F361F | 3 |
chr17:38142881-38142881 | p.A155A | 2 |
chr17:38152588-38152588 | p.V491V | 2 |
chr17:38142894-38142894 | p.L160V | 2 |
chr17:38137364-38137364 | p.S47S | 2 |
chr17:38151682-38151682 | p.R408C | 2 |
chr17:38152592-38152592 | p.? | 2 |
chr17:38142927-38142927 | p.V171M | 2 |
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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 | 3 |   | 5 |   |   | 3 |   | 1 |   |   | 8 | 3 | 1 |   |   | 8 | 5 |   | 12 |
# mutation | 2 | 3 |   | 6 |   |   | 3 |   | 1 |   |   | 8 | 3 | 1 |   |   | 6 | 5 |   | 12 |
nonsynonymous SNV |   | 1 |   | 6 |   |   | 1 |   | 1 |   |   | 7 | 2 | 1 |   |   | 3 | 3 |   | 11 |
synonymous SNV | 2 | 2 |   |   |   |   | 2 |   |   |   |   | 1 | 1 |   |   |   | 3 | 2 |   | 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 |
chr17:38151308 | p.F361F | 3 |
chr17:38146409 | p.R314C | 2 |
chr17:38151480 | p.E520Q | 2 |
chr17:38153787 | p.Y166C | 2 |
chr17:38142913 | p.G383V | 2 |
chr17:38140673 | p.A116V | 2 |
chr17:38142926 | p.G152G | 1 |
chr17:38146397 | p.T308T | 1 |
chr17:38140722 | p.F482L | 1 |
chr17:38151536 | p.A155V | 1 |
Other DBs for Point Mutations |
Copy Number for PSMD3 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 PSMD3 |
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 |
BSND,MIEN1,C2orf54,CASC3,ERBB2,GRB7,GSDMB, IRGC,LOC90110,MED1,MED24,MFSD2A,MSL1,ORMDL3, PGAP3,PPP1R1B,PSMD3,RPL19,STARD3,THRA,ZFP57 | ABCF1,ABCF3,ATP5D,AP5S1,RABL6,ESRRA,GPC1, KEAP1,NTMT1,MRPL12,NDUFV1,NOL3,PSMB5,PSMD3, PTGES2,SNRNP25,SPAG7,STK11,STOML2,TACO1,USP5 | ||||
AATF,MIEN1,CASC3,CDC6,ERBB2,FXYD2,GRB7, MED24,MSL1,ORMDL3,PGAP3,PPP1R1B,PSMD3,RAPGEFL1, RGSL1,SNAR-A2,STARD3,TCAP,THRA,UGT1A6,WIPF2 | ARF1,ATP5B,CDK2AP2,CKMT1B,CSTF2,DBNL,GNG5, HDAC1,HN1,LMAN2,MAP2K6,MPDU1,NDUFA9,OSTF1, PSMC4,PSMD3,SQRDL,TALDO1,TMEM53,TMEM54,TPM3 |
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 PSMD3 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Organism-specific databases | PharmGKB | PA38123; -. |
Organism-specific databases | CTD | 5709; -. |
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, 3 | approved; nutraceutical | Adenosine triphosphate |
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Cross referenced IDs for PSMD3 |
* 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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