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 PSMF1
Basic gene info.Gene symbolPSMF1
Gene nameproteasome (prosome, macropain) inhibitor subunit 1 (PI31)
SynonymsPI31
CytomapUCSC genome browser: 20p13
Genomic locationchr20 :1093905-1148426
Type of geneprotein-coding
RefGenesNM_006814.3,
NM_178578.2,NM_178579.1,
Ensembl idENSG00000125818
DescriptionhPI31proteasome inhibitor PI31 subunitproteasome inhibitor hP131 subunit
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000125818
HPRD : 17919
Vega : OTTHUMG00000031656
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMF1
BioGPS: 9491
Gene Expression Atlas: ENSG00000125818
The Human Protein Atlas: ENSG00000125818
PathwayNCI Pathway Interaction Database: PSMF1
KEGG: PSMF1
REACTOME: PSMF1
ConsensusPathDB
Pathway Commons: PSMF1
MetabolismMetaCyc: PSMF1
HUMANCyc: PSMF1
RegulationEnsembl's Regulation: ENSG00000125818
miRBase: chr20 :1,093,905-1,148,426
TargetScan: NM_006814
cisRED: ENSG00000125818
ContextiHOP: PSMF1
cancer metabolism search in PubMed: PSMF1
UCL Cancer Institute: PSMF1
Assigned class in ccmGDBC

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Phenotypic Information for PSMF1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMF1
Familial Cancer Database: PSMF1
* 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: PSMF1
MedGen: PSMF1 (Human Medical Genetics with Condition)
ClinVar: PSMF1
PhenotypeMGI: PSMF1 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMF1

Mutations for PSMF1
* 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
pancreasPSMF1chr2011306141130814PSMF1chr2011304661130666
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 PSMF1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW170550CLTB1565175843305175843360PSMF1544702011157951145721
AI418115FAIM3831021207080440207080459PSMF11024032011457251146026
AA309217RGL153751183843614183843636PSMF1684202011025991102943
BP249774SGTA13281927671622783271PSMF13195882011453421145610

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      1      
GAIN (# sample)   1      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=3

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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=12)
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
chr20:1106168-1106168p.L53M2
chr20:1106243-1106243p.L78F2
chr20:1145091-1145091p.P245P2
chr20:1108092-1108092p.A102A2
chr20:1099523-1099523p.F36C2
chr20:1115942-1115942p.P182S1
chr20:1108122-1108122p.I112I1
chr20:1143792-1143792p.P190P1
chr20:1106170-1106170p.L53L1
chr20:1108137-1108137p.L117L1

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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
# sample11 6  2 1  422  13 5
# mutation11 6  2 1  442  13 6
nonsynonymous SNV1  6  2    421   2 4
synonymous SNV 1      1   21  11 2
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
chr20:1106243p.P245P,PSMF12
chr20:1145091p.L78F,PSMF12
chr20:1145099p.T84T,PSMF11
chr20:1115875p.R204L,PSMF11
chr20:1145707p.S88I,PSMF11
chr20:1106263p.P212P,PSMF11
chr20:1115883p.A102T,PSMF11
chr20:1145715p.P229Q,PSMF11
chr20:1106274p.N107K,PSMF11
chr20:1115884p.Y111C,PSMF11

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 PSMF1 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 PSMF1

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

AP5S1,TMEM230,CSNK2A1,FAM110A,FASTKD5,FKBP1A,IDH3B,
MKKS,NOP56,NRSN2,NSFL1C,PANK2,PSMF1,RBCK1,
SNRPB,SOX12,SRXN1,STK35,TRIB3,VPS16,ZCCHC3
ARPC1A,ATP5E,ATP5L,ATRAID,COMMD9,COX6A1,EIF3K,
MRPL10,OST4,PDZD11,PSMB1,PSMB4,PSMB7,PSMF1,
RNASEK,RNF181,RPS20,STX8,TOMM22,TRAPPC2L,ZDHHC4

ANKEF1,AP5S1,CENPB,CRLS1,CSNK2A1,DDRGK1,ESF1,
FAM110A,FKBP1A,IDH3B,NSFL1C,PANK2,PSMF1,PTPRA,
RBCK1,STK35,TASP1,TBC1D20,TRMT6,UBOX5,ZCCHC3
ALKBH4,C12orf10,CCDC101,CUEDC2,DGCR6L,DRG2,EEF1D,
EIF3G,ERCC1,PPIE,PSMF1,R3HCC1,RAD23A,RPL12,
SIRT2,THOC5,TIMM22,UBL7,UBXN1,VPS72,WDR83
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 PSMF1


There's no related Drug.
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Cross referenced IDs for PSMF1
* 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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