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 PSMD11
Basic gene info.Gene symbolPSMD11
Gene nameproteasome (prosome, macropain) 26S subunit, non-ATPase, 11
SynonymsRpn6|S9|p44.5
CytomapUCSC genome browser: 17q11.2
Genomic locationchr17 :30771501-30808042
Type of geneprotein-coding
RefGenesNM_001270482.1,
NM_002815.3,
Ensembl idENSG00000108671
Description26S proteasome non-ATPase regulatory subunit 1126S proteasome regulatory subunit 926S proteasome regulatory subunit RPN626S proteasome regulatory subunit S926S proteasome regulatory subunit p44.5
Modification date20141207
dbXrefs MIM : 604449
HGNC : HGNC
Ensembl : ENSG00000108671
HPRD : 05119
Vega : OTTHUMG00000132811
ProteinUniProt: O00231
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMD11
BioGPS: 5717
Gene Expression Atlas: ENSG00000108671
The Human Protein Atlas: ENSG00000108671
PathwayNCI Pathway Interaction Database: PSMD11
KEGG: PSMD11
REACTOME: PSMD11
ConsensusPathDB
Pathway Commons: PSMD11
MetabolismMetaCyc: PSMD11
HUMANCyc: PSMD11
RegulationEnsembl's Regulation: ENSG00000108671
miRBase: chr17 :30,771,501-30,808,042
TargetScan: NM_001270482
cisRED: ENSG00000108671
ContextiHOP: PSMD11
cancer metabolism search in PubMed: PSMD11
UCL Cancer Institute: PSMD11
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PSMD11(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMD11
Familial Cancer Database: PSMD11
* 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 604449; gene.
Orphanet
DiseaseKEGG Disease: PSMD11
MedGen: PSMD11 (Human Medical Genetics with Condition)
ClinVar: PSMD11
PhenotypeMGI: PSMD11 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMD11

Mutations for PSMD11
* 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 PSMD11 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI291788LINC003408711262205408022054105PSMD11112458173080090430806905
BF083127PSMD11662173080629230806348PSMD1155222173079610430800878
AW835516PSMD11161180173077741330777432CTNND1165564115753650757537167

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  
LOSS (# sample)                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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=34)
Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr17:30791555-30791555p.L136S3
chr17:30804556-30804556p.C289C2
chr17:30804557-30804557p.V290M2
chr17:30791091-30791091p.E115K2
chr17:30791132-30791132p.A128A2
chr17:30796143-30796143p.S192Y2
chr17:30774048-30774048p.K59N2
chr17:30791554-30791554p.L136L2
chr17:30806861-30806861p.?2
chr17:30807212-30807212p.H375N2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22 9  3 2  511  13 7
# mutation22 6  3 2  511  13 7
nonsynonymous SNV22 4  1 2  51    2 6
synonymous SNV   2  2      1  11 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
chr17:30791555p.L136S,PSMD113
chr17:30804557p.V290M,PSMD112
chr17:30791554p.L136L,PSMD112
chr17:30796051p.D161D,PSMD112
chr17:30771555p.V7L,PSMD111
chr17:30791552p.S230L,PSMD111
chr17:30771560p.R20L,PSMD111
chr17:30806301p.S241C,PSMD111
chr17:30771600p.D25V,PSMD111
chr17:30806346p.M260V,PSMD111

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 PSMD11 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 PSMD11

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

TEFM,C17orf75,CDK5R1,CES1,CES1P1,CSHL1,DDX52,
DUSP14,EME1,KPNA2,LIN28A,MYO1D,PSMD11,PSMD12,
PSMD14,RAB11FIP4,RHOT1,SPAG5,SUZ12,UTP6,ZNF207
DNAJA4,DUSP3,EPM2A,FYCO1,IDE,KLHL31,KPNA1,
KPNA3,MFN2,NDUFS1,NRD1,OGDH,PRKAR2A,PSMC2,
PSMD11,PSMD2,PSMD7,SAR1B,SIX1,TACC2,UBE3C

ATAD5,BLMH,COPRS,EFTUD2,EIF4A3,EPR1,GOSR1,
KPNB1,LIG3,NCAPH,NMT1,POLDIP2,PSMD11,PSME3,
RAD51D,SPAG5,SUZ12,ALYREF,TUBG1,UTP18,UTP6
CAP1,CEACAM1,DHRS9,GDPD3,GHITM,GNAI3,HSPA4,
KRT20,NAT1,NT5C3A,PLAC8,PSMD11,PSMD1,RALB,
SEC61G,TPM3,TPMT,TTC39B,VDAC2,VPS26A,YWHAB
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 PSMD11
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA33902; -.
Organism-specific databasesCTD 5717; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00171proteasome (prosome, macropain) 26S subunit, non-ATPase, 11approved; nutraceuticalAdenosine triphosphate


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Cross referenced IDs for PSMD11
* 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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