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 PSMD5
Basic gene info.Gene symbolPSMD5
Gene nameproteasome (prosome, macropain) 26S subunit, non-ATPase, 5
SynonymsS5B
CytomapUCSC genome browser: 9q33.2
Genomic locationchr9 :123578331-123605206
Type of geneprotein-coding
RefGenesNM_001270427.1,
NM_005047.3,
Ensembl idENSG00000095261
Description26S protease subunit S5 basic26S proteasome non-ATPase regulatory subunit 526S proteasome subunit S5B
Modification date20141207
dbXrefs MIM : 604452
HGNC : HGNC
Ensembl : ENSG00000095261
HPRD : 05121
Vega : OTTHUMG00000020573
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMD5
BioGPS: 5711
Gene Expression Atlas: ENSG00000095261
The Human Protein Atlas: ENSG00000095261
PathwayNCI Pathway Interaction Database: PSMD5
KEGG: PSMD5
REACTOME: PSMD5
ConsensusPathDB
Pathway Commons: PSMD5
MetabolismMetaCyc: PSMD5
HUMANCyc: PSMD5
RegulationEnsembl's Regulation: ENSG00000095261
miRBase: chr9 :123,578,331-123,605,206
TargetScan: NM_001270427
cisRED: ENSG00000095261
ContextiHOP: PSMD5
cancer metabolism search in PubMed: PSMD5
UCL Cancer Institute: PSMD5
Assigned class in ccmGDBC

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Phenotypic Information for PSMD5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMD5
Familial Cancer Database: PSMD5
* 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: PSMD5
MedGen: PSMD5 (Human Medical Genetics with Condition)
ClinVar: PSMD5
PhenotypeMGI: PSMD5 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMD5

Mutations for PSMD5
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 PSMD5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI005318PSMD571489123579420123579560PSMD51393379123579158123579355
BU607444PSMD5181899123578631123578802PSMD51844219123578901123579138

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=25)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=2)
There's no deleted 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
chr9:123586946-123586947p.G278fs*82
chr9:123586959-123586959p.F273F2
chr9:123589136-123589136p.R241*2
chr9:123605126-123605126p.E21G2
chr9:123591452-123591452p.S199F1
chr9:123583640-123583640p.Y370C1
chr9:123594214-123594214p.I110V1
chr9:123591454-123591454p.E198E1
chr9:123583670-123583670p.R360T1
chr9:123595605-123595605p.I101I1

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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
# sample11 5    11 1    33 11
# mutation11 5    11 1    33 11
nonsynonymous SNV11 3            23 7
synonymous SNV   3    11 1    1  4
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
chr9:123586959p.F230F,PSMD52
chr9:123593673p.I426T,PSMD51
chr9:123586876p.E155E,PSMD51
chr9:123593680p.N422N,PSMD51
chr9:123586940p.N166S1
chr9:123593720p.T376T,PSMD51
chr9:123586941p.E164K1
chr9:123593725p.Y327C,PSMD51
chr9:123580190p.S150S1
chr9:123593733p.R298H,PSMD51

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 PSMD5 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 PSMD5

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

C9orf152,FAM206A,INIP,CDK5RAP2,FBXW2,FEM1C,GPR107,
KIAA0368,NCBP1,PDCL,PSMD5,RAB14,RABGAP1,RAD23B,
SEC16A,SLC31A1,SPTLC1,SRBD1,STX17,ZBTB43,ZNF189
API5,ARFIP1,CANX,CTBS,FNBP1L,CMTR2,LMBR1,
POT1,PSMD5,SERP1,SLC33A1,SLC39A9,TM9SF2,TMEM33,
TMEM87B,UBR7,USP3,VPS4B,ZNF138,ZNF626,ZNF737

ALG2,FAM206A,INIP,CEP78,DNAJC25,GLE1,HIATL1,
ISCA1,ISCA1P1,MRPL50,POLE3,PPP6C,PRPF4,PSMD5,
RAB14,RAD23B,RBM18,SPTLC1,TEX10,UBQLN1,ZNF484
API5,ASCC1,CDC73,CNBP,COPS2,CUL2,DARS,
DBR1,ST13P4,FAM175B,MATR3,MOCS2,MTMR6,PSMD5,
RBM18,RBMXL1,SEC62,SNX2,SYPL1,TMEM167B,UQCRB
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 PSMD5


There's no related Drug.
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Cross referenced IDs for PSMD5
* 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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