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 PSMD7
Basic gene info.Gene symbolPSMD7
Gene nameproteasome (prosome, macropain) 26S subunit, non-ATPase, 7
SynonymsMOV34|P40|Rpn8|S12
CytomapUCSC genome browser: 16q22.3
Genomic locationchr16 :74330672-74340186
Type of geneprotein-coding
RefGenesNM_002811.4,
Ensembl idENSG00000103035
Description26S proteasome non-ATPase regulatory subunit 726S proteasome regulatory subunit S1226S proteasome regulatory subunit rpn8Moloney leukemia virus-34 proviral integrationMov34 homologproteasome (prosome, macropain) 26S subunit, non-ATPase, 7 (Mov34 homo
Modification date20141207
dbXrefs MIM : 157970
HGNC : HGNC
Ensembl : ENSG00000103035
HPRD : 01147
Vega : OTTHUMG00000137601
ProteinUniProt: P51665
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMD7
BioGPS: 5713
Gene Expression Atlas: ENSG00000103035
The Human Protein Atlas: ENSG00000103035
PathwayNCI Pathway Interaction Database: PSMD7
KEGG: PSMD7
REACTOME: PSMD7
ConsensusPathDB
Pathway Commons: PSMD7
MetabolismMetaCyc: PSMD7
HUMANCyc: PSMD7
RegulationEnsembl's Regulation: ENSG00000103035
miRBase: chr16 :74,330,672-74,340,186
TargetScan: NM_002811
cisRED: ENSG00000103035
ContextiHOP: PSMD7
cancer metabolism search in PubMed: PSMD7
UCL Cancer Institute: PSMD7
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PSMD7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMD7
Familial Cancer Database: PSMD7
* 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 157970; gene.
Orphanet
DiseaseKEGG Disease: PSMD7
MedGen: PSMD7 (Human Medical Genetics with Condition)
ClinVar: PSMD7
PhenotypeMGI: PSMD7 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMD7

Mutations for PSMD7
* 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
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 PSMD7 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF858256KLK3168195136144151361508PSMD763146167433084574334055

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=20)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr16:74339242-74339242p.H196Y2
chr16:74339301-74339301p.V215V2
chr16:74334091-74334091p.S51S2
chr16:74339460-74339460p.S268S2
chr16:74335019-74335019p.Y79C1
chr16:74338294-74338294p.?1
chr16:74330842-74330842p.V10V1
chr16:74339461-74339461p.V269M1
chr16:74335475-74335475p.W94*1
chr16:74339215-74339215p.L187M1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 2    2  431 115 8
# mutation 1 1    2  431 115 8
nonsynonymous SNV 1      2  431   3 5
synonymous SNV   1           112 3
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
chr16:74339391p.S51S2
chr16:74334091p.F245F2
chr16:74336135p.A164A1
chr16:74339317p.V10V1
chr16:74330842p.V170L1
chr16:74336158p.L17F1
chr16:74339345p.R177Q1
chr16:74330861p.G27S1
chr16:74336163p.D207H1
chr16:74339361p.V35G1

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 PSMD7 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 PSMD7

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

AARS,CMC2,CFAP20,CENPN,CFDP1,CIAPIN1,CIRH1A,
COG4,EMC8,DDX19A,DHX38,DUS2,EXOSC6,KARS,
NAE1,NIP7,NUP93,PSMD7,SF3B3,VAC14,VPS4A
PRADC1,CHCHD3,FEZ2,FUNDC2,HSPB7,HTATSF1,MAP4,
NDUFB3,OPTN,PGK1,PINK1,PSMC2,PSMD1,PSMD2,
PSMD7,RNF10,SGCG,SNTA1,UBE2D4,WSB2,YBX1

CFDP1,CIRH1A,COG4,EMC8,DDX19A,DNAJA3,E2F4,
HSBP1,KARS,MPHOSPH6,NAE1,NIP7,NUDT21,NUTF2,
PDF,POLR2C,PSMA7,PSMD7,SLC7A6OS,USP10,VPS4A
CCDC167,EIF2B3,EIF2S2,ENSA,ERH,GOLT1B,HAT1,
MORF4L2,PSMA1,PSMA3,PSMA4,PSMA7,PSMC2,PSMD14,
PSMD6,PSMD7,SARNP,SNRPB2,SNRPE,SSBP1,TCEB1
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 PSMD7


There's no related Drug.
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Cross referenced IDs for PSMD7
* 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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