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 PSMD8
Basic gene info.Gene symbolPSMD8
Gene nameproteasome (prosome, macropain) 26S subunit, non-ATPase, 8
SynonymsHEL-S-91n|HIP6|HYPF|Nin1p|Rpn12|S14|p31
CytomapUCSC genome browser: 19q13.2
Genomic locationchr19 :38865189-38874464
Type of geneprotein-coding
RefGenesNM_002812.4,
Ensembl idENSG00000099341
Description26S proteasome non-ATPase regulatory subunit 826S proteasome regulatory subunit RPN1226S proteasome regulatory subunit S1426S proteasome regulatory subunit p31epididymis secretory sperm binding protein Li 91n
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000099341
HPRD : 10171
Vega : OTTHUMG00000150691
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMD8
BioGPS: 5714
Gene Expression Atlas: ENSG00000099341
The Human Protein Atlas: ENSG00000099341
PathwayNCI Pathway Interaction Database: PSMD8
KEGG: PSMD8
REACTOME: PSMD8
ConsensusPathDB
Pathway Commons: PSMD8
MetabolismMetaCyc: PSMD8
HUMANCyc: PSMD8
RegulationEnsembl's Regulation: ENSG00000099341
miRBase: chr19 :38,865,189-38,874,464
TargetScan: NM_002812
cisRED: ENSG00000099341
ContextiHOP: PSMD8
cancer metabolism search in PubMed: PSMD8
UCL Cancer Institute: PSMD8
Assigned class in ccmGDBC

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Phenotypic Information for PSMD8(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMD8
Familial Cancer Database: PSMD8
* 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: PSMD8
MedGen: PSMD8 (Human Medical Genetics with Condition)
ClinVar: PSMD8
PhenotypeMGI: PSMD8 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMD8

Mutations for PSMD8
* 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
ovaryPSMD8chr193887012938870149PSMD8chr193887229638872316
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 PSMD8 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DW427896PSMD817109193886683638867047HDLBP1102772242195674242196041
AA437370PSMD8163193887440238874464SLC35B25344564422241544222808
BF093758ITGAL1412163051811930525166PSMD8410497193886612238866209
AX794816ITGAL1412163051811930525166PSMD8410497193886612238866209
BC071826ELF2454474140035878140036280PSMD84481392193886543538874115

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=10)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr19:38871622-38871622p.I169I2
chr19:38869956-38869956p.V112L1
chr19:38873891-38873891p.?1
chr19:38869972-38869972p.T117M1
chr19:38873894-38873894p.R213Q1
chr19:38865566-38865566p.L16I1
chr19:38869973-38869973p.T117T1
chr19:38873943-38873943p.Q229Q1
chr19:38865574-38865574p.K18K1
chr19:38869976-38869976p.E118D1

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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 1 3  1  1       3 3
# mutation 1 2  1  1       3 3
nonsynonymous SNV 1 1     1       2 1
synonymous SNV   1  1          1 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
chr19:38869973p.T210T2
chr19:38873943p.L109I1
chr19:38874011p.K135N1
chr19:38865566p.L194L1
chr19:38866844p.L196I1
chr19:38869925p.T257T1
chr19:38869929p.Y302Y1
chr19:38871607p.A303T1
chr19:38872859p.R306Q1
chr19:38872860p.Q322Q1

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 PSMD8 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 PSMD8

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

ACTN4,C19orf47,ECH1,EID2,EIF3K,FAM98C,FBL,
MRPS12,PAF1,POLR2I,PSMC4,PSMD8,RPS16,SARS2,
SHKBP1,SIRT2,SPINT2,SUPT5H,TIMM50,TMEM147,YIF1B
CNPPD1,GPX4,HINT2,LOC729991,MRPL24,MRPL46,MRPS11,
MRPS15,NDUFAF3,NDUFB8,PARK7,POLR2E,POLR2L,PSMA7,
PSMD8,SLC2A4RG,SOD1,TALDO1,TESK1,TST,UROD

AP2S1,ATP5SL,COX6B1,EIF3K,GEMIN7,MED31,MRPL54,
MRPS12,NDUFB7,NOSIP,OAZ1,POLR2I,PRMT1,PSMC4,
PSMD8,RPS16,RPS5,SDHAF1,SNRPD2,TIMM50,YIF1B
CHCHD2,CKLF,DAD1,HAX1,LAMTOR5,MRPL22,MRPL52,
MYEOV2,NDUFA6,NDUFA7,NDUFB4,NDUFB6,PHF5A,POLR2F,
PSMA7,PSMD8,PSMD9,RBX1,STOML2,TIMM8B,UFD1L
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 PSMD8


There's no related Drug.
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Cross referenced IDs for PSMD8
* 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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