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 PSMC1
Basic gene info.Gene symbolPSMC1
Gene nameproteasome (prosome, macropain) 26S subunit, ATPase, 1
SynonymsP26S4|S4|p56
CytomapUCSC genome browser: 14q32.11
Genomic locationchr14 :90722893-90738966
Type of geneprotein-coding
RefGenesNM_002802.2,
Ensembl idENSG00000100764
Description26S protease regulatory subunit 426S proteasome AAA-ATPase subunit RPT2proteasome 26S ATPase subunit 1proteasome 26S subunit ATPase 1proteasome 26S subunit, ATPase, 1
Modification date20141207
dbXrefs MIM : 602706
HGNC : HGNC
Ensembl : ENSG00000100764
HPRD : 04084
Vega : OTTHUMG00000171019
ProteinUniProt: P62191
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMC1
BioGPS: 5700
Gene Expression Atlas: ENSG00000100764
The Human Protein Atlas: ENSG00000100764
PathwayNCI Pathway Interaction Database: PSMC1
KEGG: PSMC1
REACTOME: PSMC1
ConsensusPathDB
Pathway Commons: PSMC1
MetabolismMetaCyc: PSMC1
HUMANCyc: PSMC1
RegulationEnsembl's Regulation: ENSG00000100764
miRBase: chr14 :90,722,893-90,738,966
TargetScan: NM_002802
cisRED: ENSG00000100764
ContextiHOP: PSMC1
cancer metabolism search in PubMed: PSMC1
UCL Cancer Institute: PSMC1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PSMC1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMC1
Familial Cancer Database: PSMC1
* 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 602706; gene.
Orphanet
DiseaseKEGG Disease: PSMC1
MedGen: PSMC1 (Human Medical Genetics with Condition)
ClinVar: PSMC1
PhenotypeMGI: PSMC1 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMC1

Mutations for PSMC1
* 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
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasPSMC1chr149073230790732327PSMC1chr149073467790734697
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 PSMC1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB102097PSMC11469149072290690730159SYTL147055112767396627674047

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 # sample1     1          
GAIN (# sample)                 
LOSS (# sample)1     1          
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=19)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr14:90735826-90735826p.G323R2
chr14:90735856-90735856p.R333R2
chr14:90731485-90731485p.V222V1
chr14:90729661-90729661p.?1
chr14:90735888-90735888p.R343S1
chr14:90730154-90730154p.L143Q1
chr14:90734664-90734664p.G263V1
chr14:90729701-90729701p.L65S1
chr14:90736545-90736545p.R346H1
chr14:90730172-90730172p.S149L1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  41 1 2  1    26 7
# mutation1  41 1 2  1    26 8
nonsynonymous SNV1  41   1  1    16 7
synonymous SNV      1 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
chr14:90736610p.P219S1
chr14:90730065p.K258R1
chr14:90734664p.G263V1
chr14:90738656p.R268Q1
chr14:90730089p.H9R1
chr14:90734679p.H277Y1
chr14:90730104p.L65S1
chr14:90734705p.P279L1
chr14:90730154p.L102L1
chr14:90734712p.G291W1

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 PSMC1 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 PSMC1

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

APOPT1,SLIRP,IFT43,C14orf2,CINP,COMMD1,COX6B1,
GADD45GIP1,MRPL52,MRPS24,LINC00152,NDUFB11,NDUFB1,NUDT1,
PSMB1,PSMC1,PSMG3,RNF181,RPL36AL,SIVA1,USMG5
ATP5H,ATP5J,ATP6V1E1,COX14,APOPT1,MINOS1,SMIM20,
FUNDC2,GTF3A,LOC150381,MRPL40,MSRB2,NDUFA12,NDUFA6,
NDUFB1,PFDN1,PSMB1,PSMC1,SNAPIN,TTC1,YBX1

AHSA1,SLIRP,IFT43,C14orf2,CHMP4A,CINP,DHRS4L2,
ERH,FKBP3,GLRX5,GSTZ1,MED6,NEDD8,NGDN,
OSGEP,PSMA3,PSMA6,PSMB5,PSMC1,RPL36AL,SIVA1
ANXA4,ARPC2,ATP5E,COX17,DERL2,GDI2,IL7,
MRPS18C,PGAM1,PGAM4,POMP,PPP1R7,PRDX1,PSMC1,
SEC61G,SF3B14,SHFM1,SOD1,SUGT1,SUMO1P3,TSPAN8
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 PSMC1


There's no related Drug.
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Cross referenced IDs for PSMC1
* 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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