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 PSMD2
Basic gene info.Gene symbolPSMD2
Gene nameproteasome (prosome, macropain) 26S subunit, non-ATPase, 2
SynonymsP97|RPN1|S2|TRAP2
CytomapUCSC genome browser: 3q27.1
Genomic locationchr3 :184017021-184026840
Type of geneprotein-coding
RefGenesNM_001278708.1,
NM_001278709.1,NM_002808.4,
Ensembl idENSG00000175166
Description26S proteasome non-ATPase regulatory subunit 255.11 proteinTNFR-associated protein 2protein 55.11tumor necrosis factor type 1 receptor-associated protein 2
Modification date20141207
dbXrefs MIM : 606223
HGNC : HGNC
Ensembl : ENSG00000175166
HPRD : 05870
Vega : OTTHUMG00000156796
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMD2
BioGPS: 5708
Gene Expression Atlas: ENSG00000175166
The Human Protein Atlas: ENSG00000175166
PathwayNCI Pathway Interaction Database: PSMD2
KEGG: PSMD2
REACTOME: PSMD2
ConsensusPathDB
Pathway Commons: PSMD2
MetabolismMetaCyc: PSMD2
HUMANCyc: PSMD2
RegulationEnsembl's Regulation: ENSG00000175166
miRBase: chr3 :184,017,021-184,026,840
TargetScan: NM_001278708
cisRED: ENSG00000175166
ContextiHOP: PSMD2
cancer metabolism search in PubMed: PSMD2
UCL Cancer Institute: PSMD2
Assigned class in ccmGDBC

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Phenotypic Information for PSMD2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMD2
Familial Cancer Database: PSMD2
* 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: PSMD2
MedGen: PSMD2 (Human Medical Genetics with Condition)
ClinVar: PSMD2
PhenotypeMGI: PSMD2 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMD2

Mutations for PSMD2
* 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 PSMD2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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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=40)
Stat. for Synonymous SNVs
(# total SNVs=18)
Stat. for Deletions
(# total SNVs=2)
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
chr3:184020156-184020156p.?3
chr3:184024196-184024196p.D621E2
chr3:184017699-184017699p.?2
chr3:184025278-184025278p.Y723C2
chr3:184025435-184025435p.R746H2
chr3:184021749-184021749p.L446L2
chr3:184018174-184018174p.R100H2
chr3:184019697-184019697p.R181Q2
chr3:184025217-184025217p.R703*1
chr3:184020504-184020504p.H301Y1

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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
# sample 2181 7 2  64  1715 12
# mutation 2181 7 2  74  1718 12
nonsynonymous SNV 215  3 2  42  1214 9
synonymous SNV   31 4    32   54 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
chr3:184019697p.L758F,PSMD22
chr3:184026613p.R100H2
chr3:184018174p.R616H,PSMD22
chr3:184025435p.R51Q,PSMD22
chr3:184026538p.G552E,PSMD21
chr3:184022098p.K728N,PSMD21
chr3:184019696p.V110M,PSMD21
chr3:184024258p.L355L,PSMD21
chr3:184025484p.R557Q,PSMD21
chr3:184020522p.T733A,PSMD21

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 PSMD2 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 PSMD2

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

ABCF3,ACTL6A,ALG3,AP2M1,DCUN1D1,DNAJB11,DVL3,
ECE2,EIF4G1,FBXO45,FXR1,GMPS,LSG1,PCYT1A,
PLK1,PSMD2,RFC4,SENP5,TBCCD1,WDR53,YEATS2
PRADC1,C6orf106,CDK16,HAGH,KIF1C,MAP4,NDUFA8,
NFE2L1,OGDH,PGK1,PINK1,PRKACA,PSMC2,PSMD2,
PSMD7,RNF10,SDHA,SNTA1,VCP,WBSCR16,ZFAND3

ABCF3,CCNF,CLSPN,COPB2,DNMT1,DTX3L,EIF4G1,
INCENP,EMC1,KIAA1524,KLHL18,KPNA1,MCM2,NAA50,
NUP210,PCYT1A,PLK1,PSMD1,PSMD2,RNF168,SHCBP1
ACTR3,ADRM1,CALR,CAP1,CARS,CEACAM6,ENO1,
OR52I1,PCBP1,PGAM1,PLIN3,PSMB2,PSMC3,PSMC4,
PSMD1,PSMD2,PSMD3,RALB,SNORA45B,TARS,TFG
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 PSMD2
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
DB00188proteasome (prosome, macropain) 26S subunit, non-ATPase, 2approved; investigationalBortezomib


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Cross referenced IDs for PSMD2
* 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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