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 PSMA7
Basic gene info.Gene symbolPSMA7
Gene nameproteasome (prosome, macropain) subunit, alpha type, 7
SynonymsC6|HSPC|RC6-1|XAPC7
CytomapUCSC genome browser: 20q13.33
Genomic locationchr20 :60711790-60718474
Type of geneprotein-coding
RefGenesNM_002792.3,
NM_152255.1,
Ensembl idENSG00000101182
Descriptionproteasome subunit RC6-1proteasome subunit XAPC7proteasome subunit alpha 4proteasome subunit alpha type-7
Modification date20141207
dbXrefs MIM : 606607
HGNC : HGNC
Ensembl : ENSG00000101182
HPRD : 05967
Vega : OTTHUMG00000032895
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMA7
BioGPS: 5688
Gene Expression Atlas: ENSG00000101182
The Human Protein Atlas: ENSG00000101182
PathwayNCI Pathway Interaction Database: PSMA7
KEGG: PSMA7
REACTOME: PSMA7
ConsensusPathDB
Pathway Commons: PSMA7
MetabolismMetaCyc: PSMA7
HUMANCyc: PSMA7
RegulationEnsembl's Regulation: ENSG00000101182
miRBase: chr20 :60,711,790-60,718,474
TargetScan: NM_002792
cisRED: ENSG00000101182
ContextiHOP: PSMA7
cancer metabolism search in PubMed: PSMA7
UCL Cancer Institute: PSMA7
Assigned class in ccmGDBC

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Phenotypic Information for PSMA7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMA7
Familial Cancer Database: PSMA7
* 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: PSMA7
MedGen: PSMA7 (Human Medical Genetics with Condition)
ClinVar: PSMA7
PhenotypeMGI: PSMA7 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMA7

Mutations for PSMA7
* 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 PSMA7 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
EC492083NCL1572232325512232325571PSMA751101206071325760713308
BQ685104PSMA710225206071416760714965RBBP7226889X1687062416876965
BG474310TESC227512117476879117484452PSMA7274669206071199460714913
AA581992PSMA71180206071179060711972UBA52167528191868266918685899
CA312659PSMA78176206071195260713278PSMA7175240206071326160713326
BF237904PSMA716127206071418560714879PSMA7125434206071195260714202

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=9)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr20:60713265-60713265p.D185Y2
chr20:60713283-60713283p.E179K2
chr20:60714232-60714232p.R124C2
chr20:60714888-60714888p.E99E2
chr20:60712444-60712444p.V210V1
chr20:60714901-60714901p.R95Q1
chr20:60714933-60714933p.I84I1
chr20:60715998-60715998p.V33V1
chr20:60714163-60714163p.T147S1
chr20:60718271-60718271p.S30L1

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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
# sample21 2     1 2     5 3
# mutation21 2     1 2     4 3
nonsynonymous SNV   1     1 1     4 2
synonymous SNV21 1       1       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
chr20:60713265p.D185Y2
chr20:60714232p.R124C2
chr20:60712444p.V210V1
chr20:60714933p.E179K1
chr20:60715998p.Y145C1
chr20:60713283p.G140G1
chr20:60718345p.F127L1
chr20:60714168p.T119M1
chr20:60714182p.K115T1
chr20:60714221p.E99E1

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 PSMA7 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 PSMA7

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

ADRM1,ARFGAP1,ARFRP1,ATP5E,GID8,MRGBP,C20orf24,
DUS2,FAM96B,MTG2,LSM14B,OGFR,OSBPL2,PSMA7,
RPS21,TAF4,NELFCD,ALYREF,TMEM208,TPD52L2,TUBA1C
ACADS,ARL2,ATP5I,BLOC1S1,BSG,ETFB,FPGS,
MPST,MRPL41,MRPL46,MRPL53,MRPS11,MRPS15,NDUFA2,
NDUFB8,POLR2E,PSMA7,PSMD8,SLC2A4RG,TALDO1,TMEM120A

ADRM1,AHCY,ATP5E,MRGBP,C20orf24,RTFDC1,COMMD7,
DPM1,EIF2S2,EIF6,ERGIC3,PDRG1,PFDN4,PSMA7,
RAE1,RALY,ROMO1,RPS21,NELFCD,TP53RK,TPD52L2
EMC7,MRPL20,MRPL52,MYEOV2,NEDD8,PHF5A,PSMA1,
PSMA5,PSMA7,PSMB1,PSMD13,PSMD14,PSMD8,RBX1,
SNRPG,SSBP1,STRA13,TCEB1,TIMM8B,TOMM5,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 PSMA7
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, 7experimentalN-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB07558proteasome (prosome, macropain) subunit, alpha type, 7experimental2-ACETYLAMINO-4-METHYL-PENTANOIC ACID [1-(1-FORMYL-PENTYLCARBAMOYL)-3-METHYL-BUTYL]-AMIDE
DB08515proteasome (prosome, macropain) subunit, alpha type, 7experimental(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, 7approved; nutraceuticalAdenosine triphosphate


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Cross referenced IDs for PSMA7
* 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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