Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for PSMD3
Basic gene info.Gene symbolPSMD3
Gene nameproteasome (prosome, macropain) 26S subunit, non-ATPase, 3
SynonymsP58|RPN3|S3|TSTA2
CytomapUCSC genome browser: 17q21.1
Genomic locationchr17 :38137059-38154212
Type of geneprotein-coding
RefGenesNM_002809.3,
Ensembl idENSG00000108344
Description26S proteasome non-ATPase regulatory subunit 326S proteasome regulatory subunit RPN326S proteasome regulatory subunit S3proteasome subunit p58tissue specific transplantation antigen 2
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000108344
HPRD : 10170
Vega : OTTHUMG00000133251
ProteinUniProt: O43242
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMD3
BioGPS: 5709
Gene Expression Atlas: ENSG00000108344
The Human Protein Atlas: ENSG00000108344
PathwayNCI Pathway Interaction Database: PSMD3
KEGG: PSMD3
REACTOME: PSMD3
ConsensusPathDB
Pathway Commons: PSMD3
MetabolismMetaCyc: PSMD3
HUMANCyc: PSMD3
RegulationEnsembl's Regulation: ENSG00000108344
miRBase: chr17 :38,137,059-38,154,212
TargetScan: NM_002809
cisRED: ENSG00000108344
ContextiHOP: PSMD3
cancer metabolism search in PubMed: PSMD3
UCL Cancer Institute: PSMD3
Assigned class in ccmGDBB - This gene belongs to cancer gene.

Top
Phenotypic Information for PSMD3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMD3
Familial Cancer Database: PSMD3
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PSMD3
MedGen: PSMD3 (Human Medical Genetics with Condition)
ClinVar: PSMD3
PhenotypeMGI: 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasPSMD3chr173813835638138376PSMD3chr173813873638138756
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PSMD3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BC001684PSMD391359173813707238151531PRELID1134922565176730830176733662
BQ361077MIB253357115610501561355PSMD3355595173814599038146394
BM824189ASAP113878131124494131124568PSMD382165173815377838153861
AW376286CHURC12352146540607565406426PSMD3352478173814601038146136

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2  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)

Top
check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=5

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=46)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr17:38151480-38151480p.G383V4
chr17:38140673-38140673p.A116V3
chr17:38151308-38151308p.F361F3
chr17:38142881-38142881p.A155A2
chr17:38152588-38152588p.V491V2
chr17:38142894-38142894p.L160V2
chr17:38137364-38137364p.S47S2
chr17:38151682-38151682p.R408C2
chr17:38152592-38152592p.?2
chr17:38142927-38142927p.V171M2

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample23 5  3 1  831  85 12
# mutation23 6  3 1  831  65 12
nonsynonymous SNV 1 6  1 1  721  33 11
synonymous SNV22    2    11   32 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])

Top
check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr17:38151308p.F361F3
chr17:38146409p.R314C2
chr17:38151480p.E520Q2
chr17:38153787p.Y166C2
chr17:38142913p.G383V2
chr17:38140673p.A116V2
chr17:38142926p.G152G1
chr17:38146397p.T308T1
chr17:38140722p.F482L1
chr17:38151536p.A155V1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy 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]

Top
Gene Expression for PSMD3

check002.gifGene 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.

check002.gifDifferential 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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

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
check002.gifCo-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

: Open all plots for all cancer types

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for PSMD3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA38123; -.
Organism-specific databasesCTD 5709; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00171proteasome (prosome, macropain) 26S subunit, non-ATPase, 3approved; nutraceuticalAdenosine triphosphate


Top
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

: Open all cross reference information



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas