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 PSMA4
Basic gene info.Gene symbolPSMA4
Gene nameproteasome (prosome, macropain) subunit, alpha type, 4
SynonymsHC9|HsT17706|PSC9
CytomapUCSC genome browser: 15q25.1
Genomic locationchr15 :78832746-78841563
Type of geneprotein-coding
RefGenesNM_001102667.1,
NM_001102668.1,NM_002789.4,
Ensembl idENSG00000041357
Descriptionmacropain subunit C9multicatalytic endopeptidase complex subunit C9proteasome component C9proteasome subunit HC9proteasome subunit Lproteasome subunit alpha type-4
Modification date20141207
dbXrefs MIM : 176846
HGNC : HGNC
Ensembl : ENSG00000041357
HPRD : 10168
Vega : OTTHUMG00000143859
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMA4
BioGPS: 5685
Gene Expression Atlas: ENSG00000041357
The Human Protein Atlas: ENSG00000041357
PathwayNCI Pathway Interaction Database: PSMA4
KEGG: PSMA4
REACTOME: PSMA4
ConsensusPathDB
Pathway Commons: PSMA4
MetabolismMetaCyc: PSMA4
HUMANCyc: PSMA4
RegulationEnsembl's Regulation: ENSG00000041357
miRBase: chr15 :78,832,746-78,841,563
TargetScan: NM_001102667
cisRED: ENSG00000041357
ContextiHOP: PSMA4
cancer metabolism search in PubMed: PSMA4
UCL Cancer Institute: PSMA4
Assigned class in ccmGDBC

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Phenotypic Information for PSMA4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMA4
Familial Cancer Database: PSMA4
* 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: PSMA4
MedGen: PSMA4 (Human Medical Genetics with Condition)
ClinVar: PSMA4
PhenotypeMGI: PSMA4 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMA4

Mutations for PSMA4
* 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 PSMA4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU190440PSMA42311157884121278841523PSAP304820107357837373579633
AW149658RAB3122761898622759862549PSMA4267622157884116478841518

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=15)
Stat. for Synonymous SNVs
(# total SNVs=1)
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
chr15:78834927-78834927p.R50H2
chr15:78841258-78841258p.E253G1
chr15:78834954-78834954p.V59A1
chr15:78837990-78837990p.G131C1
chr15:78834977-78834977p.K67E1
chr15:78838104-78838104p.A169S1
chr15:78834992-78834992p.?1
chr15:78838948-78838950p.E181delE1
chr15:78836557-78836557p.I79L1
chr15:78838990-78838990p.I194S1

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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
# sample   2    2  211   2 2
# mutation   2    2  211   3 2
nonsynonymous SNV   1    2  211   3 2
synonymous SNV   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
chr15:78837238p.A42V,PSMA41
chr15:78837261p.G60C,PSMA41
chr15:78837990p.A98S,PSMA41
chr15:78838104p.I123S,PSMA41
chr15:78838990p.V132V,PSMA41
chr15:78839018p.K158E,PSMA41
chr15:78834894p.R178C,PSMA41
chr15:78841185p.R178H,PSMA41
chr15:78834926p.A39V,PSMA41
chr15:78841245p.R50S,PSMA41

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 PSMA4 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 PSMA4

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

HYKK,BOLA3,COX5A,FAM103A1,FBXO22,FBXO22-AS1,IDH3A,
IMP3,MORF4L1,MRPS11,MTHFS,PSMA3,PSMA4,PSMA5,
PSMD14,RCN2,SNRPA1,SNRPG,SNUPN,TIPIN,WDR61
ARPC2,CMC2,C20orf24,CCDC53,CDC123,EIF2S2,GTF3C6,
LSM3,MRPL47,NOP10,POMP,PSMA1,PSMA3,PSMA4,
PSMA5,PSMA6,RBX1,SNRPG,TOMM5,TTC1,ZBTB8OS

EMC7,CCNB2,DUT,ERH,FAM96A,FBXO22,KIAA0101,
MRPL46,MRPS11,MTHFS,NOP10,OIP5,PSMA3,PSMA4,
PSMA5,PSMA6,RAB11A,SEC11A,SRSF3,TIPIN,WDR61
C1GALT1C1,DYNLT1,EIF5A,EIF5AL1,ERH,GOLT1B,NMI,
POMP,PPA1,PSMA1,PSMA2,PSMA3,PSMA4,PSMA5,
PSMA6,PSMA7,PSMB1,PSMB4,RASL11A,SARNP,TMSB10
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 PSMA4
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, 4experimentalN-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB08515proteasome (prosome, macropain) subunit, alpha type, 4experimental(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, 4approved; nutraceuticalAdenosine triphosphate


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Cross referenced IDs for PSMA4
* 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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