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 PSMA5
Basic gene info.Gene symbolPSMA5
Gene nameproteasome (prosome, macropain) subunit, alpha type, 5
SynonymsPSC5|ZETA
CytomapUCSC genome browser: 1p13
Genomic locationchr1 :109941652-109969108
Type of geneprotein-coding
RefGenesNM_001199772.1,
NM_001199773.1,NM_001199774.1,NM_002790.3,
Ensembl idENSG00000143106
Descriptionmacropain subunit zetamacropain zeta chainmulticatalytic endopeptidase complex zeta chainproteasome alpha 5 subunitproteasome component 5proteasome subunit alpha type-5proteasome subunit zetaproteasome zeta chain
Modification date20141207
dbXrefs MIM : 176844
HGNC : HGNC
Ensembl : ENSG00000143106
HPRD : 01464
Vega : OTTHUMG00000012001
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMA5
BioGPS: 5686
Gene Expression Atlas: ENSG00000143106
The Human Protein Atlas: ENSG00000143106
PathwayNCI Pathway Interaction Database: PSMA5
KEGG: PSMA5
REACTOME: PSMA5
ConsensusPathDB
Pathway Commons: PSMA5
MetabolismMetaCyc: PSMA5
HUMANCyc: PSMA5
RegulationEnsembl's Regulation: ENSG00000143106
miRBase: chr1 :109,941,652-109,969,108
TargetScan: NM_001199772
cisRED: ENSG00000143106
ContextiHOP: PSMA5
cancer metabolism search in PubMed: PSMA5
UCL Cancer Institute: PSMA5
Assigned class in ccmGDBC

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Phenotypic Information for PSMA5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMA5
Familial Cancer Database: PSMA5
* 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: PSMA5
MedGen: PSMA5 (Human Medical Genetics with Condition)
ClinVar: PSMA5
PhenotypeMGI: PSMA5 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMA5

Mutations for PSMA5
* 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
breastPSMA5chr1109961538109961538PSMA5chr1109964437109964437
ovaryPSMA5chr1109944206109944226ZC3H18chr168868332988683349
ovaryPSMA5chr1109946699109946719SORT1chr1109925311109925331
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 PSMA5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP284679PSMA514421109954767109969062USF14325881161012649161015686

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=11)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=1)
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
chr1:109957929-109957929p.E51E2
chr1:109953692-109953692p.R168*1
chr1:109957948-109957948p.G45D1
chr1:109954503-109954503p.Q152*1
chr1:109957979-109957979p.S35T1
chr1:109954510-109954510p.K149K1
chr1:109964523-109964523p.G19R1
chr1:109944642-109944642p.D240A1
chr1:109954749-109954750p.S117fs*301
chr1:109964529-109964529p.P17S1

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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
# sample12 51       1   31 1
# mutation12 41       1   31 1
nonsynonymous SNV11 31       1   21 1
synonymous SNV 1 2            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
chr1:109955744p.S21S,PSMA52
chr1:109957929p.S6F1
chr1:109957934p.I180M,PSMA51
chr1:109957948p.K138T,PSMA51
chr1:109944647p.M131R,PSMA51
chr1:109964523p.S53S,PSMA51
chr1:109952611p.F43F,PSMA51
chr1:109964529p.T38I,PSMA51
chr1:109952632p.E7D,PSMA51
chr1:109968936p.E51E1

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 PSMA5 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 PSMA5

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

ALG3,ATP5F1,BOLA3,C20orf24,LAMTOR5,MRPS15,PSMA2,
PSMA4,PSMA5,PSMB2,PSMC1,PSMD14,PSME2,PSRC1,
PTTG1,SARS,SNRPC,SNRPG,TALDO1,TUBA1C,WDR77
CDC123,CHCHD1,CIAPIN1,DYNLT1,ERH,H2AFZ,HN1,
JTB,MAD2L1BP,MRPL17,MRPS23,NUTF2,PSMA4,PSMA5,
RBX1,SLC35B1,SNRPG,SSBP1,TMEM147,TXNDC17,UCHL3

AK2,ATP5F1,BCAS2,COX7A2,EBNA1BP2,EIF3I,LAMTOR5,
LSM2,MRPL22,MRPS15,MRPS18C,PHF5A,PPIH,PSMA4,
PSMA5,PSMA6,RAN,TIMM8B,TOMM22,UQCRQ,VPS29
EMC7,CKS1B,MRPL52,PGK1,POMP,PSMA1,PSMA2,
PSMA3,PSMA4,PSMA5,PSMA6,PSMA7,PSMB1,PSMD13,
PSMD14,RBX1,RPL26L1,SNRPG,STRA13,TMSB10,TOMM5
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 PSMA5
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB07475proteasome (prosome, macropain) subunit, alpha type, 5experimentalN-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB08515proteasome (prosome, macropain) subunit, alpha type, 5experimental(3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE
DB00171proteasome (prosome, macropain) subunit, alpha type, 5approved; nutraceuticalAdenosine triphosphate


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Cross referenced IDs for PSMA5
* 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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