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 PSMC4
Basic gene info.Gene symbolPSMC4
Gene nameproteasome (prosome, macropain) 26S subunit, ATPase, 4
SynonymsMIP224|RPT3|S6|TBP-7|TBP7
CytomapUCSC genome browser: 19q13.11-q13.13
Genomic locationchr19 :40477072-40487353
Type of geneprotein-coding
RefGenesNM_006503.3,
NM_153001.2,
Ensembl idENSG00000013275
Description26S protease regulatory subunit 6B26S proteasome AAA-ATPase subunit RPT3MB67-interacting proteinTat-binding protein 7protease 26S subunit 6
Modification date20141207
dbXrefs MIM : 602707
HGNC : HGNC
Ensembl : ENSG00000013275
HPRD : 04085
Vega : OTTHUMG00000182577
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMC4
BioGPS: 5704
Gene Expression Atlas: ENSG00000013275
The Human Protein Atlas: ENSG00000013275
PathwayNCI Pathway Interaction Database: PSMC4
KEGG: PSMC4
REACTOME: PSMC4
ConsensusPathDB
Pathway Commons: PSMC4
MetabolismMetaCyc: PSMC4
HUMANCyc: PSMC4
RegulationEnsembl's Regulation: ENSG00000013275
miRBase: chr19 :40,477,072-40,487,353
TargetScan: NM_006503
cisRED: ENSG00000013275
ContextiHOP: PSMC4
cancer metabolism search in PubMed: PSMC4
UCL Cancer Institute: PSMC4
Assigned class in ccmGDBC

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Phenotypic Information for PSMC4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMC4
Familial Cancer Database: PSMC4
* 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: PSMC4
MedGen: PSMC4 (Human Medical Genetics with Condition)
ClinVar: PSMC4
PhenotypeMGI: PSMC4 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMC4

Mutations for PSMC4
* 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 PSMC4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP432759MXD4987422597082263498PSMC487369194048597640486604
BQ219974ELL31479154408454444086239PSMC4479557194048033640480497
AI143487PSMC410124194048723340487348WNT7B121186224631630646316371
BU674697PSMC417138194048723340487353PSMC4138339194048634340487225
BU608468PSMC417126194048723540487344PSMC4121265194048709840487242
CV361424PSMC41134194048583440486052PSMC4131476194047707240478447

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample                1
GAIN (# sample)                1
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=39)
Stat. for Synonymous SNVs
(# total SNVs=15)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=2)

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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
chr19:40485861-40485861p.A271T4
chr19:40478338-40478338p.K66N3
chr19:40487161-40487161p.A402A2
chr19:40487178-40487178p.K408T2
chr19:40480235-40480235p.I119I2
chr19:40477113-40477113p.E2K2
chr19:40480653-40480654p.R200fs*432
chr19:40480659-40480659p.P199P2
chr19:40485749-40485749p.S233S2
chr19:40478056-40478056p.E14K1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13 4  1  2 721 156 11
# mutation13 4  1  2 721 146 10
nonsynonymous SNV 3 3  1    42   12 9
synonymous SNV1  1     2 3 1 134 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
chr19:40478338p.K66N3
chr19:40485861p.I119I,PSMC42
chr19:40480235p.A271T,PSMC42
chr19:40478337p.L68L1
chr19:40486259p.H221H,PSMC41
chr19:40480516p.S355S,PSMC41
chr19:40485749p.T100I,PSMC41
chr19:40486287p.R229Q,PSMC41
chr19:40480518p.K369N,PSMC41
chr19:40485783p.T107T,PSMC41

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 PSMC4 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 PSMC4

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

AKT2,C19orf47,COX6B1,EID2,EIF3K,FBL,LRFN1,
MAP3K10,MRPS12,NFKBIB,PAF1,PSMC4,PSMD8,RPS16,
SARS2,SHKBP1,SIRT2,SPINT2,SUPT5H,TIMM50,YIF1B
ADRM1,ASNA1,ATP6V0D1,COPE,FAM58A,LSM4,NAA38,
MRPL28,PPP1CA,PPP1R14B,PSMB6,PSMC4,ROMO1,SEC13,
SLC39A3,TBCB,TSPAN17,TUBB4B,USP5,YIF1A,YIF1B

ALKBH6,AP2S1,BCL2L12,C19orf47,COX6B1,EGLN2,EID2,
LIN37,MRPS12,NFKBIB,PDCD2L,PDCD5,POLR2I,PRMT1,
PSENEN,PSMC4,PSMD8,RBM42,RUVBL2,TIMM50,YIF1B
ACTR3,ADRM1,ASS1,CALR,CASP5,CRELD2,DNAJB11,
PDIA6,PGK1,POMP,PSMA1,PSMA3,PSMB2,PSMB3,
PSMC4,PSMD13,PSMD2,RPN1,SDF2L1,SEC61B,TMED9
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 PSMC4
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
DB00877proteasome (prosome, macropain) 26S subunit, ATPase, 4approved; investigationalSirolimus


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Cross referenced IDs for PSMC4
* 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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