Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 PSMD6
Basic gene info.Gene symbolPSMD6
Gene nameproteasome (prosome, macropain) 26S subunit, non-ATPase, 6
SynonymsRpn7|S10|SGA-113M|p42A|p44S10
CytomapUCSC genome browser: 3p14.1
Genomic locationchr3 :63996230-64009120
Type of geneprotein-coding
RefGenesNM_001271779.1,
NM_001271780.1,NM_001271781.1,NM_014814.2,
Ensembl idENSG00000163636
Description26S proteasome non-ATPase regulatory subunit 6breast cancer-associated protein SGA-113Mphosphonoformate immuno-associated protein 4proteasome regulatory particle subunit p44S10
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000163636
HPRD : 18370
Vega : OTTHUMG00000158765
ProteinUniProt: Q15008
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMD6
BioGPS: 9861
Gene Expression Atlas: ENSG00000163636
The Human Protein Atlas: ENSG00000163636
PathwayNCI Pathway Interaction Database: PSMD6
KEGG: PSMD6
REACTOME: PSMD6
ConsensusPathDB
Pathway Commons: PSMD6
MetabolismMetaCyc: PSMD6
HUMANCyc: PSMD6
RegulationEnsembl's Regulation: ENSG00000163636
miRBase: chr3 :63,996,230-64,009,120
TargetScan: NM_001271779
cisRED: ENSG00000163636
ContextiHOP: PSMD6
cancer metabolism search in PubMed: PSMD6
UCL Cancer Institute: PSMD6
Assigned class in ccmGDBB - This gene belongs to cancer gene.

Top
Phenotypic Information for PSMD6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMD6
Familial Cancer Database: PSMD6
* 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: PSMD6
MedGen: PSMD6 (Human Medical Genetics with Condition)
ClinVar: PSMD6
PhenotypeMGI: PSMD6 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMD6

Mutations for PSMD6
* 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 PSMD6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA942713PSMD6128136400805064009080EIF3A27358210120802239120809487
CD626170PSMD6347136400500764009108ZNF646471693163108878331089005
CD626167ZNF64613240163108878331089010PSMD624054136400805664009108
CD626168PSMD6347236400500764009108ZNF646472680163108878331088997
CD626169ZNF64613240163108878331089010PSMD624069936400501964009108
CD626166PSMD61548436400500764009108ZNF646484670163108878331088971

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
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.

Top
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=6

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr3:64008049-64008049p.E99G4
chr3:63996436-63996436p.D360N2
chr3:64005033-64005033p.R146R2
chr3:64009039-64009039p.I19M2
chr3:64004505-64004505p.L236F2
chr3:64004514-64004514p.R233G2
chr3:64008050-64008050p.E99K2
chr3:64004282-64004282p.Q273H2
chr3:64004323-64004323p.L260L1
chr3:64004969-64004969p.?1

Top
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
# sample 2 12    1  21  113 3
# mutation 2 7    1  21  113 3
nonsynonymous SNV 2 5    1  2   1 2 3
synonymous SNV   3        1   11  
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])

Top
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
chr3:64008049p.E61G,PSMD64
chr3:64004505p.L198F,PSMD63
chr3:64008051p.S60R,PSMD62
chr3:64004980p.S231F,PSMD61
chr3:64004295p.K55N,PSMD61
chr3:64005106p.R229R,PSMD61
chr3:64004300p.L43S,PSMD61
chr3:64007994p.R229C,PSMD61
chr3:64004302p.L222L,PSMD61
chr3:64008044p.H213Y,PSMD61

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 PSMD6 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]

Top
Gene Expression for PSMD6

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ANO10,APEH,ARF4,C3orf14,CMC1,GNL3,NDUFV2,
NPRL2,PDE12,PDHB,PSMD6,RFT1,RHOA,RPP14,
SELK,SHQ1,SPCS1,THOC7,TUSC2,UBA3,UQCRC1
ATP5C1,ATP5F1,BOLA3,SLIRP,CMC2,COPS4,COX7B,
EIF2S2,GLRX5,LAMTOR5,MRPL47,NDUFAB1,NDUFB1,NDUFB4,
NDUFB6,NDUFV2,PSMA3,PSMA6,PSMD14,PSMD6,TCEB1

BRIX1,CCDC58,TMA7,CCNB1,DYNC1LI1,GNL3,KCTD6,
LSM3,MRPL47,PDCD10,PDHB,PSMA1,PSMD14,PSMD6,
SRSF3,SPCS1,TAF9,TBCA,THOC7,UBA3,UBE2N
MCMBP,COPS4,EIF2B3,EIF2S1,HAT1,MAGOHB,MORF4L2,
MRPS10,PPIL1,PSMC2,PSMD14,PSMD6,PSMD7,RAN,
SNRPB2,SSBP1,TCEB1,TIMM17A,TOMM5,UBE2N,VBP1
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for PSMD6


There's no related Drug.
Top
Cross referenced IDs for PSMD6
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas