Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 PSME4
Basic gene info.Gene symbolPSME4
Gene nameproteasome (prosome, macropain) activator subunit 4
SynonymsPA200
CytomapUCSC genome browser: 2p16.2
Genomic locationchr2 :54091203-54197977
Type of geneprotein-coding
RefGenesNM_014614.2,
Ensembl idENSG00000068878
Descriptionproteasome activator 200 kDaproteasome activator PA200proteasome activator complex subunit 4
Modification date20141207
dbXrefs MIM : 607705
HGNC : HGNC
Ensembl : ENSG00000068878
HPRD : 09652
Vega : OTTHUMG00000151852
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSME4
BioGPS: 23198
Gene Expression Atlas: ENSG00000068878
The Human Protein Atlas: ENSG00000068878
PathwayNCI Pathway Interaction Database: PSME4
KEGG: PSME4
REACTOME: PSME4
ConsensusPathDB
Pathway Commons: PSME4
MetabolismMetaCyc: PSME4
HUMANCyc: PSME4
RegulationEnsembl's Regulation: ENSG00000068878
miRBase: chr2 :54,091,203-54,197,977
TargetScan: NM_014614
cisRED: ENSG00000068878
ContextiHOP: PSME4
cancer metabolism search in PubMed: PSME4
UCL Cancer Institute: PSME4
Assigned class in ccmGDBC

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Phenotypic Information for PSME4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSME4
Familial Cancer Database: PSME4
* 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: PSME4
MedGen: PSME4 (Human Medical Genetics with Condition)
ClinVar: PSME4
PhenotypeMGI: PSME4 (International Mouse Phenotyping Consortium)
PhenomicDB: PSME4

Mutations for PSME4
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
ovaryPSME4chr25416982854169848chr21722401517224035
ovaryPSME4chr25417690954176929chr213581668335816703
ovaryPSME4chr25418508954185109ACYP2chr25435018754350207
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 PSME4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG430921SMEK2217725584258655844398PSME417384525409247254096679

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample          1  1  1
GAIN (# sample)          1  1  1
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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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

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=122)
Stat. for Synonymous SNVs
(# total SNVs=34)
Stat. for Deletions
(# total SNVs=5)
Stat. for Insertions
(# total SNVs=1)

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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
chr2:54093345-54093345p.T1691fs*>394
chr2:54167140-54167140p.?3
chr2:54154547-54154547p.R412I3
chr2:54153116-54153116p.F432F3
chr2:54120871-54120871p.L1212L2
chr2:54127040-54127040p.E1020*2
chr2:54147425-54147425p.E661E2
chr2:54150237-54150237p.L529L2
chr2:54128521-54128521p.H970R2
chr2:54094006-54094006p.R1645C2

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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
# sample41 141 8 2321794  99 18
# mutation41 181 8 23221114  912 22
nonsynonymous SNV31 151 4 2221584  59 17
synonymous SNV1  3  4  1 63   43 5
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
chr2:54154547p.F546F3
chr2:54153116p.R526I3
chr2:54147481p.R914Q1
chr2:54164553p.G741C1
chr2:54114518p.A1790E1
chr2:54125075p.L388L1
chr2:54153153p.I1526I1
chr2:54117299p.E170K1
chr2:54131196p.R1340Q1
chr2:54159206p.L1159L1

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 PSME4 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 PSME4

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

ACTR2,ADAM17,ATL2,EML4,GMPS,KCMF1,KPNA4,
MSH2,MSH6,MTIF2,PLCH1,PPP1CB,PPP3R1,PSME4,
R3HDM1,SMEK2,SRPK1,SUV39H2,SYNCRIP,TTK,WDR43
ANK3,BARD1,ENAH,FAM160A1,G3BP2,HSPA14,IARS,
MAPK6,MARS2,NAA15,NAA25,NAA35,NIPAL1,PDE4B,
PSME4,RPAP3,SRPK1,SSX2IP,URB2,USP54,YTHDC2

ATAD2B,BIRC6,DHX57,DNAJC10,EPT1,FAM98A,FBXO11,
GEN1,IWS1,MRPL19,POLR1A,POLR1B,PPM1G,PSME4,
R3HDM1,SAP130,SMC6,TET3,TRAF3IP1,UGGT1,USP34
ASCC3,ATR,DHX29,EIF4G1,EPRS,FUBP1,HNRNPA3,
IDE,KPNB1,POP1,PSME4,SEC23IP,SFPQ,SRSF1,
SYNCRIP,TARDBP,TRIP12,UGGT1,UTP20,XPO5,YWHAG
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 PSME4


There's no related Drug.
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Cross referenced IDs for PSME4
* 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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