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 PSMC2
Basic gene info.Gene symbolPSMC2
Gene nameproteasome (prosome, macropain) 26S subunit, ATPase, 2
SynonymsMSS1|Nbla10058|S7
CytomapUCSC genome browser: 7q22.1-q22.3
Genomic locationchr7 :102987970-103002914
Type of geneprotein-coding
RefGenesNM_001204453.1,
NM_002803.3,
Ensembl idENSG00000161057
Description26S protease regulatory subunit 726S proteasome AAA-ATPase subunit RPT1mammalian suppressor of sgv-1 of yeastprotease 26S subunit 7proteasome 26S subunit ATPase 2proteasome 26S subunit, ATPase, 2putative protein product of Nbla10058
Modification date20141207
dbXrefs MIM : 154365
HGNC : HGNC
Ensembl : ENSG00000161057
HPRD : 01105
Vega : OTTHUMG00000157206
ProteinUniProt: P35998
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMC2
BioGPS: 5701
Gene Expression Atlas: ENSG00000161057
The Human Protein Atlas: ENSG00000161057
PathwayNCI Pathway Interaction Database: PSMC2
KEGG: PSMC2
REACTOME: PSMC2
ConsensusPathDB
Pathway Commons: PSMC2
MetabolismMetaCyc: PSMC2
HUMANCyc: PSMC2
RegulationEnsembl's Regulation: ENSG00000161057
miRBase: chr7 :102,987,970-103,002,914
TargetScan: NM_001204453
cisRED: ENSG00000161057
ContextiHOP: PSMC2
cancer metabolism search in PubMed: PSMC2
UCL Cancer Institute: PSMC2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PSMC2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMC2
Familial Cancer Database: PSMC2
* 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 154365; gene.
Orphanet
DiseaseKEGG Disease: PSMC2
MedGen: PSMC2 (Human Medical Genetics with Condition)
ClinVar: PSMC2
PhenotypeMGI: PSMC2 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMC2

Mutations for PSMC2
* 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 PSMC2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM983260PSMC218757103008545103008602PSMC2732297103008158103008401
DA326202PSMC222237102988112102995381APC2185495112177806112178137
BF985831CGA1729068779522487795497PSMC22834157103008430103008562
AU118024GTF3C423239135559279135559600PSMC23237547102988089103002475
BQ315283PSMC273797103004625103008013PTPRF37442814401078444010838

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=30)
Stat. for Synonymous SNVs
(# total SNVs=13)
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
chr7:103006556-103006556p.A264P2
chr7:103004631-103004631p.G211G2
chr7:103008218-103008218p.R369K2
chr7:103004703-103004703p.A235A2
chr7:103003148-103003148p.K146K2
chr7:103004748-103004748p.V250V2
chr7:103003152-103003152p.Q148E2
chr7:102996218-102996218p.E90*2
chr7:103006538-103006538p.R258C2
chr7:102996237-102996237p.A96V2

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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
# sample5125  4 41 24   27 4
# mutation11125  4 41 24   27 4
nonsynonymous SNV8 13  3 2  24   25 3
synonymous SNV3112  1 21       2 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
chr7:103004631p.G211G2
chr7:103004703p.A235A2
chr7:103006538p.S387S1
chr7:102996162p.Q88H,PSMC21
chr7:103008184p.G251G1
chr7:103003194p.C389Y1
chr7:103006539p.A104V,PSMC21
chr7:102996164p.R258C1
chr7:103008218p.I397M1
chr7:103004624p.A119V,PSMC21

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 PSMC2 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 PSMC2

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

ARMC10,ARPC1A,ATP5C1,ATP5J2,CMC2,CENPN,DBF4,
DNAJC2,MGC72080,ORC5,PSMA2,PSMB2,PSMC2,PSMD14,
RHEB,RINT1,SHFM1,SLC25A13,SNRPG,SSBP1,TUBA1C
PRADC1,C6orf106,FAM118B,FEZ2,FUNDC2,ICMT,LDHA,
MAP4,NDUFB3,PGK1,PRKACA,PSMC2,PSMD14,PSMD1,
PSMD2,PSMD7,SETD3,SGCG,SYNPO,UBE2D4,WSB2

AP4M1,ARMC10,ATP5J2,ATP6V1F,BUD31,MALSU1,CAPZA2,
CDK5,CHCHD2,COPS6,DBF4,GTPBP10,ORC5,PMPCB,
POP7,PSMA2,PSMC2,RHEB,RINT1,RPA3,SSBP1
CCDC167,COPS4,EIF2S2,HAT1,MORF4L2,MRPL20,PSMA1,
PSMA2,PSMA3,PSMA7,PSMB1,PSMB5,PSMB6,PSMC2,
PSMC3,PSMD14,PSMD6,PSMD7,RPL22L1,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 PSMC2


There's no related Drug.
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Cross referenced IDs for PSMC2
* 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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