Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 PSMD4
Basic gene info.Gene symbolPSMD4
Gene nameproteasome (prosome, macropain) 26S subunit, non-ATPase, 4
SynonymsAF|AF-1|ASF|MCB1|Rpn10|S5A|pUB-R5
CytomapUCSC genome browser: 1q21.3
Genomic locationchr1 :151227196-151239954
Type of geneprotein-coding
RefGenesNM_002810.2,
NM_153822.2,
Ensembl idENSG00000159352
Description26S proteasome non-ATPase regulatory subunit 426S proteasome regulatory subunit S5AS5a/antisecretory factor proteinangiocidinantisecretory factor 1multiubiquitin chain-binding protein
Modification date20141207
dbXrefs MIM : 601648
HGNC : HGNC
Ensembl : ENSG00000159352
HPRD : 03386
Vega : OTTHUMG00000012349
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMD4
BioGPS: 5710
Gene Expression Atlas: ENSG00000159352
The Human Protein Atlas: ENSG00000159352
PathwayNCI Pathway Interaction Database: PSMD4
KEGG: PSMD4
REACTOME: PSMD4
ConsensusPathDB
Pathway Commons: PSMD4
MetabolismMetaCyc: PSMD4
HUMANCyc: PSMD4
RegulationEnsembl's Regulation: ENSG00000159352
miRBase: chr1 :151,227,196-151,239,954
TargetScan: NM_002810
cisRED: ENSG00000159352
ContextiHOP: PSMD4
cancer metabolism search in PubMed: PSMD4
UCL Cancer Institute: PSMD4
Assigned class in ccmGDBC

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Phenotypic Information for PSMD4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMD4
Familial Cancer Database: PSMD4
* 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: PSMD4
MedGen: PSMD4 (Human Medical Genetics with Condition)
ClinVar: PSMD4
PhenotypeMGI: 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.

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
pancreasPSMD4chr1151236464151236484PI4KBchr1151295275151295295
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 PSMD4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU590293RPS91325195470544754711372PSMD43125061151239761151239955
BU538390C20orf2713352037345883735159PSMD43356701151237348151238086
U51007IQGAP17128159104534491045467PSMD411913231151227233151239865

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

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check002.gifCopy 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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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr1:151234659-151234659p.R17W2
chr1:151237890-151237890p.L153L1
chr1:151238796-151238796p.A259V1
chr1:151237896-151237896p.A155A1
chr1:151238867-151238867p.E283Q1
chr1:151234661-151234661p.R17R1
chr1:151237918-151237918p.K163E1
chr1:151238873-151238873p.E285K1
chr1:151234711-151234711p.N34S1
chr1:151237936-151237936p.H169Y1

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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
# sample12 31 3 2  51   22 3
# mutation12 41 3 2  51   22 4
nonsynonymous SNV12 21 1 2  11   21 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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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
chr1:151234661p.R17R2
chr1:151237896p.R17W1
chr1:151239681p.A241A1
chr1:151234659p.A259V1
chr1:151237918p.N34S1
chr1:151239726p.R272H1
chr1:151237936p.T88M1
chr1:151239749p.E283Q1
chr1:151234711p.R91R1
chr1:151237951p.D309Y1

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 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

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

: Open all plots for all cancer types


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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

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
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

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check002.gifInteracting Genes (from Pathway Commons)

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

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Pharmacological Information for PSMD4
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

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, 4approved; nutraceuticalAdenosine 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

: Open all cross reference information



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