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 PSMC5
Basic gene info.Gene symbolPSMC5
Gene nameproteasome (prosome, macropain) 26S subunit, ATPase, 5
SynonymsS8|SUG-1|SUG1|TBP10|TRIP1|p45|p45/SUG
CytomapUCSC genome browser: 17q23.3
Genomic locationchr17 :61904769-61909387
Type of geneprotein-coding
RefGenesNM_001199163.1,
NM_002805.5,
Ensembl idENSG00000087191
Description26S protease regulatory subunit 826S proteasome AAA-ATPase subunit RPT6MSUG1 proteinTat-binding protein homolog 10proteasome 26S ATPase subunit 5proteasome 26S subunit ATPase 5proteasome subunit p45thyroid hormone receptor-interacting protein 1thy
Modification date20141207
dbXrefs MIM : 601681
HGNC : HGNC
Ensembl : ENSG00000087191
HPRD : 03400
Vega : OTTHUMG00000179013
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMC5
BioGPS: 5705
Gene Expression Atlas: ENSG00000087191
The Human Protein Atlas: ENSG00000087191
PathwayNCI Pathway Interaction Database: PSMC5
KEGG: PSMC5
REACTOME: PSMC5
ConsensusPathDB
Pathway Commons: PSMC5
MetabolismMetaCyc: PSMC5
HUMANCyc: PSMC5
RegulationEnsembl's Regulation: ENSG00000087191
miRBase: chr17 :61,904,769-61,909,387
TargetScan: NM_001199163
cisRED: ENSG00000087191
ContextiHOP: PSMC5
cancer metabolism search in PubMed: PSMC5
UCL Cancer Institute: PSMC5
Assigned class in ccmGDBC

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Phenotypic Information for PSMC5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMC5
Familial Cancer Database: PSMC5
* 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: PSMC5
MedGen: PSMC5 (Human Medical Genetics with Condition)
ClinVar: PSMC5
PhenotypeMGI: PSMC5 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMC5

Mutations for PSMC5
* 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 PSMC5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=16)
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
chr17:61907831-61907831p.L174L4
chr17:61906877-61906877p.Q40Q3
chr17:61907214-61907214p.R57C2
chr17:61907764-61907764p.G152V2
chr17:61907223-61907223p.R60W2
chr17:61907224-61907224p.R60L2
chr17:61907804-61907804p.I165I2
chr17:61908745-61908745p.R310H2
chr17:61907851-61907851p.A181D1
chr17:61908496-61908496p.G262fs*681

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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
# sample   91 1 2   32  44 8
# mutation   111 1 1   32  45 9
nonsynonymous SNV   9  1     31  14 6
synonymous SNV   21   1    1  31 3
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
chr17:61906877p.Q32Q,PSMC53
chr17:61907214p.R49C,PSMC52
chr17:61907223p.R52W,PSMC52
chr17:61907224p.R52L,PSMC52
chr17:61907804p.I157I,PSMC52
chr17:61908504p.G11V,PSMC51
chr17:61907825p.R193Q,PSMC51
chr17:61908517p.V354V,PSMC51
chr17:61907835p.T199T,PSMC51
chr17:61908527p.A230V,PSMC51

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 PSMC5 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 PSMC5

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

AMZ2,AMZ2P1,CEP95,CCDC47,CYB561,DDX42,DDX5,
EMC9,FTSJ3,HRAS,MAP3K3,METTL2A,MRPL38,POLG2,
PSMC5,PTRH2,SMARCD2,STRADA,TACO1,TEX2,TLK2
ARL6IP4,AURKAIP1,HYPK,TSR3,C19orf70,CDC37,CHMP2A,
COPS6,CUEDC2,FIS1,GADD45GIP1,MRPL28,NAA10,NDUFA13,
NDUFS6,PDAP1,PSMC3,PSMC5,SNF8,STUB1,UBXN6

AARSD1,ARHGDIA,ATP5H,CCDC137,DDX42,DNAJC7,FTSJ3,
GPS1,H3F3B,HGS,PSMC5,PTRH2,SAP30BP,SIRT7,
SLC25A19,SMARCD2,SNF8,STRADA,TACO1,TAF15,UBE2O
ADCYAP1,APLN,KIAA1549L,CMSS1,CCDC124,ENO1,HARS,
IFITM2,LEPREL1,NUDC,PDAP1,PFDN2,PGAM1,PSMB2,
PSMB6,PSMC3,PSMC5,S100A11,STOM,TUBG1,U2AF1
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 PSMC5


There's no related Drug.
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Cross referenced IDs for PSMC5
* 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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