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 PSME1
Basic gene info.Gene symbolPSME1
Gene nameproteasome (prosome, macropain) activator subunit 1 (PA28 alpha)
SynonymsIFI5111|PA28A|PA28alpha|REGalpha
CytomapUCSC genome browser: 14q11.2
Genomic locationchr14 :24605377-24608176
Type of geneprotein-coding
RefGenesNM_001281528.1,
NM_001281529.1,NM_006263.3,NM_176783.2,
Ensembl idENSG00000092010
Description11S regulator complex subunit alpha29-kD MCP activator subunitIGUP I-5111activator of multicatalytic protease subunit 1interferon gamma up-regulated I-5111 proteininterferon-gamma IEF SSP 5111interferon-gamma-inducible protein 5111proteasome activa
Modification date20141207
dbXrefs MIM : 600654
HGNC : HGNC
Ensembl : ENSG00000092010
HPRD : 02803
Vega : OTTHUMG00000028795
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSME1
BioGPS: 5720
Gene Expression Atlas: ENSG00000092010
The Human Protein Atlas: ENSG00000092010
PathwayNCI Pathway Interaction Database: PSME1
KEGG: PSME1
REACTOME: PSME1
ConsensusPathDB
Pathway Commons: PSME1
MetabolismMetaCyc: PSME1
HUMANCyc: PSME1
RegulationEnsembl's Regulation: ENSG00000092010
miRBase: chr14 :24,605,377-24,608,176
TargetScan: NM_001281528
cisRED: ENSG00000092010
ContextiHOP: PSME1
cancer metabolism search in PubMed: PSME1
UCL Cancer Institute: PSME1
Assigned class in ccmGDBC

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Phenotypic Information for PSME1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSME1
Familial Cancer Database: PSME1
* 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: PSME1
MedGen: PSME1 (Human Medical Genetics with Condition)
ClinVar: PSME1
PhenotypeMGI: PSME1 (International Mouse Phenotyping Consortium)
PhenomicDB: PSME1

Mutations for PSME1
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PSME1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI048257KCNE37494117417602174176041PSME181339142460600124606259
BG979539MYH930174223668194736682855PSME1173293142460635024606585
BM990679PSME119455142460740324608168IQCE447506726471302647189

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=7)
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
chr14:24607306-24607306p.N147D2
chr14:24606616-24606616p.K74K1
chr14:24607315-24607315p.V150L1
chr14:24606744-24606744p.E88*1
chr14:24607316-24607316p.V150A1
chr14:24606746-24606746p.E88E1
chr14:24607332-24607332p.?1
chr14:24606928-24606928p.V104V1
chr14:24607399-24607399p.?1
chr14:24606933-24606933p.C106Y1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21 2  2 1  1 1   1 1
# mutation21 2  2 1  1 1   1 1
nonsynonymous SNV1  1  1    1 1   1 1
synonymous SNV11 1  1 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
chr14:24606936p.V150A,PSME11
chr14:24606965p.M160I,PSME11
chr14:24606976p.G169G,PSME11
chr14:24607315p.R198W,PSME11
chr14:24607316p.A10A,PSME11
chr14:24607425p.K74K,PSME11
chr14:24607452p.E88E,PSME11
chr14:24605501p.K90N,PSME11
chr14:24607692p.N107S,PSME11
chr14:24606616p.L117V,PSME11

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 PSME1 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 PSME1

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

BST2,IFT43,CHMP4A,EMC9,GMPR2,IFI35,IRF9,
MDP1,NEDD8,NRL,PSMB10,PSMB8,PSME1,PSME2,
RABGGTA,RARRES3,RNF181,RNF31,RPL36AL,TM9SF1,UBE2L6
ARPC4,C17orf49,EIF6,GSTP1,IMP3,LSM2,LY6E,
MANF,PRELID1,PSMB10,PSMB8,PSME1,PSME2,PSMG3,
PYCARD,RAB34,RANBP1,RARRES3,SDF2,SNRPF,WDR54

EIF5A,ETV7,FBXO6,IFI27,IRF1,NAA38,MRPL52,
NMI,PSMA3,PSMA6,PSMB10,PSMB8,PSMB9,PSMD9,
PSME1,PSME2,RARRES3,RPL36AL,SCO2,TAP1,UBE2L6
C5orf15,CARD16,CASP1,EPSTI1,ETV7,FAM26F,GBP4,
IFI30,IFI35,IRF1,NMI,PSMB10,PSMB8,PSMB9,
PSME1,PSME2,RARRES3,STAT1,TAP1,TRIM21,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 PSME1


There's no related Drug.
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Cross referenced IDs for PSME1
* 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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