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 PSMA1
Basic gene info.Gene symbolPSMA1
Gene nameproteasome (prosome, macropain) subunit, alpha type, 1
SynonymsHC2|HEL-S-275|NU|PROS30
CytomapUCSC genome browser: 11p15.1
Genomic locationchr11 :14526421-14541991
Type of geneprotein-coding
RefGenesNM_001143937.1,
NM_002786.3,NM_148976.2,
Ensembl idENSG00000129084
Description30 kDa prosomal proteinPROS-30epididymis secretory protein Li 275macropain subunit C2macropain subunit numulticatalytic endopeptidase complex subunit C2proteasome component C2proteasome nu chainproteasome subunit alpha type-1proteasome subunit nu
Modification date20141207
dbXrefs MIM : 602854
HGNC : HGNC
Ensembl : ENSG00000129084
HPRD : 04170
Vega : OTTHUMG00000165825
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMA1
BioGPS: 5682
Gene Expression Atlas: ENSG00000129084
The Human Protein Atlas: ENSG00000129084
PathwayNCI Pathway Interaction Database: PSMA1
KEGG: PSMA1
REACTOME: PSMA1
ConsensusPathDB
Pathway Commons: PSMA1
MetabolismMetaCyc: PSMA1
HUMANCyc: PSMA1
RegulationEnsembl's Regulation: ENSG00000129084
miRBase: chr11 :14,526,421-14,541,991
TargetScan: NM_001143937
cisRED: ENSG00000129084
ContextiHOP: PSMA1
cancer metabolism search in PubMed: PSMA1
UCL Cancer Institute: PSMA1
Assigned class in ccmGDBC

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Phenotypic Information for PSMA1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMA1
Familial Cancer Database: PSMA1
* 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: PSMA1
MedGen: PSMA1 (Human Medical Genetics with Condition)
ClinVar: PSMA1
PhenotypeMGI: PSMA1 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMA1

Mutations for PSMA1
* 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 PSMA1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP386202SSR11313672816047281915PSMA1314500111452642414526610
DA097339PSMA11121111456192514562045PKP41195622159433781159477909

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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=1)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr11:14526779-14526779p.D251Y1
chr11:14529241-14529241p.F232F1
chr11:14539218-14539218p.A75V1

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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 2  2 1  2   142 3
# mutation11 2  2 1  2   142 3
nonsynonymous SNV11 1  2 1  2   142 1
synonymous SNV   1               2
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
chr11:14535995p.F99F,PSMA12
chr11:14539218p.A75V,PSMA12
chr11:14535155p.S160F,PSMA11
chr11:14535181p.G129C,PSMA11
chr11:14535392p.A121S1
chr11:14526746p.Q60H,PSMA11
chr11:14535931p.T42T,PSMA11
chr11:14526749p.E262K,PSMA11
chr11:14526751p.Q31R,PSMA11
chr11:14526784p.M261V,PSMA11

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 PSMA1 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 PSMA1

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

BTBD10,C11orf58,CCNB1,COPB1,GTF2H1,HTATIP2,KIF18A,
LDHA,MTCH2,PRMT3,PSMA1,PSMA2,PSMA3,PSMD14,
RRAS2,SAAL1,TALDO1,TSG101,TXNL1,VPS29,ZDHHC13
C20orf24,EIF2S2,GNG5,LSM3,MRPL47,POMP,PSMA1,
PSMA2,PSMA3,PSMA4,PSMA6,PSMD6,RHEB,SUMO1,
THOC7,TOMM5,TTC1,TXNL1,UBE2D2,UBE2V1,YWHAE

ATP5L,C11orf58,C11orf73,CCDC59,DCUN1D5,EIF3M,GLRX3,
LSM3,MRPS23,NDUFS3,POLR2G,PSMA1,PSMA2,PSMB1,
PSMD13,PSMD14,PTPMT1,SRSF3,SNRPG,TIMM8B,TMEM126A
SLIRP,EMC7,DYNLT1,PGK1,POMP,PPA1,PSMA1,
PSMA2,PSMA3,PSMA4,PSMA5,PSMA6,PSMA7,PSMB1,
PSMC2,PSMC6,PSMD13,PSMD14,RBX1,SNRPG,UFD1L
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 PSMA1
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, 1experimentalN-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB08515proteasome (prosome, macropain) subunit, alpha type, 1experimental(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, 1approved; nutraceuticalAdenosine triphosphate


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Cross referenced IDs for PSMA1
* 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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