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 PSME2
Basic gene info.Gene symbolPSME2
Gene nameproteasome (prosome, macropain) activator subunit 2 (PA28 beta)
SynonymsPA28B|PA28beta|REGbeta
CytomapUCSC genome browser: 14q11.2
Genomic locationchr14 :24612573-24615855
Type of geneprotein-coding
RefGenesNM_002818.2,
Ensembl idENSG00000100911
Description11S regulator complex beta subunit11S regulator complex subunit betaMCP activator, 31-kD subunitREG-betaactivator of multicatalytic protease subunit 2cell migration-inducing protein 22proteasome activator 28 subunit betaproteasome activator 28-beta
Modification date20141207
dbXrefs MIM : 602161
HGNC : HGNC
Ensembl : ENSG00000100911
HPRD : 03697
Vega : OTTHUMG00000028797
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSME2
BioGPS: 5721
Gene Expression Atlas: ENSG00000100911
The Human Protein Atlas: ENSG00000100911
PathwayNCI Pathway Interaction Database: PSME2
KEGG: PSME2
REACTOME: PSME2
ConsensusPathDB
Pathway Commons: PSME2
MetabolismMetaCyc: PSME2
HUMANCyc: PSME2
RegulationEnsembl's Regulation: ENSG00000100911
miRBase: chr14 :24,612,573-24,615,855
TargetScan: NM_002818
cisRED: ENSG00000100911
ContextiHOP: PSME2
cancer metabolism search in PubMed: PSME2
UCL Cancer Institute: PSME2
Assigned class in ccmGDBC

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Phenotypic Information for PSME2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSME2
Familial Cancer Database: PSME2
* 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: PSME2
MedGen: PSME2 (Human Medical Genetics with Condition)
ClinVar: PSME2
PhenotypeMGI: PSME2 (International Mouse Phenotyping Consortium)
PhenomicDB: PSME2

Mutations for PSME2
* 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
ovaryPSME2chr142461288724612907chr142463761624637636
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 PSME2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AV646791PSME22109142461446224614674ANKRD461033678101534603101534921
AV651403PSME22109142461446224614674ANKRD461033638101534607101534921
AV652105PSME22109142461446224614674ANKRD461036068101534418101534921
AV651374PSME22109142461446224614674ANKRD461033688101534602101534921
BF205135PSME2125198142461574124615814RPS2019969185698561956987051
BF884903PSME21112142461433924614642SNAP9110412368431255884312577
AW997232PSME23236142461461324615821RAB1023338322629874926298901
BG999584TGOLN22630228554810585548383PSME2301556142461328424613539

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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=12)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr14:24615447-24615447p.V17V8
chr14:24612871-24612871p.R188W2
chr14:24613439-24613439p.V153V1
chr14:24614371-24614371p.?1
chr14:24613441-24613441p.V153I1
chr14:24614455-24614455p.E87*1
chr14:24612672-24612672p.S222R1
chr14:24613443-24613443p.A152V1
chr14:24614466-24614466p.Q83L1
chr14:24612835-24612835p.G200W1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample      1  1 22  142 5
# mutation      1  1 22  142 5
nonsynonymous SNV      1  1 11   42 3
synonymous SNV           11  1   2
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
chr14:24613646p.P109S1
chr14:24613650p.Q83E1
chr14:24612672p.D81H1
chr14:24614302p.F35L1
chr14:24612835p.R34I1
chr14:24614467p.S222R1
chr14:24612869p.Q22Q1
chr14:24614473p.G200W1
chr14:24612871p.G11G1
chr14:24614958p.R188R1

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 PSME2 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 PSME2

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

APOL1,APOL2,EMC9,HLA-B,IFI35,IRF1,IRF9,
MRPL52,NEDD8,PSMA3,PSMB10,PSMB8,PSMB9,PSMC1,
PSME1,PSME2,RNF181,RNF31,RPL36AL,TRIM21,UBE2L6
LY6E,MANF,NANS,NFKBIE,PPIB,PRELID1,PSMB10,
PSMB8,PSME1,PSME2,RAB34,RANBP1,RARRES3,RNASEH2A,
RUVBL1,SDF2L1,SNRPF,SSR4,TAPBP,TOR3A,UBE2L6

APOL2,BAK1,BATF2,BST2,EIF5A,ETV7,FBXO6,
HLA-DMA,IRF1,NMI,PSMA3,PSMA6,PSMB10,PSMB8,
PSMB9,PSME1,PSME2,RARRES3,RPL36AL,TAP1,UBE2L6
APOL1,ASS1,CASP1,CXCL9,ETV7,FAM26F,GBP1,
GBP4,GBP7,GZMB,HRASLS2,IFI35,IFITM1,LAP3,
PARP9,PSMB10,PSMB9,PSME1,PSME2,STAT1,UBE2L6
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 PSME2


There's no related Drug.
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Cross referenced IDs for PSME2
* 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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