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 PSMD10
Basic gene info.Gene symbolPSMD10
Gene nameproteasome (prosome, macropain) 26S subunit, non-ATPase, 10
SynonymsdJ889N15.2|p28|p28(GANK)
CytomapUCSC genome browser: Xq22.3
Genomic locationchrX :107327434-107334874
Type of geneprotein-coding
RefGenesNM_002814.3,
NM_170750.2,
Ensembl idENSG00000101843
Description26S proteasome non-ATPase regulatory subunit 1026S proteasome regulatory subunit p28ankyrin repeat proteingankyrinhepatocellular carcinoma-associated protein p28-II
Modification date20141207
dbXrefs MIM : 300880
HGNC : HGNC
Ensembl : ENSG00000101843
HPRD : 04594
Vega : OTTHUMG00000022177
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMD10
BioGPS: 5716
Gene Expression Atlas: ENSG00000101843
The Human Protein Atlas: ENSG00000101843
PathwayNCI Pathway Interaction Database: PSMD10
KEGG: PSMD10
REACTOME: PSMD10
ConsensusPathDB
Pathway Commons: PSMD10
MetabolismMetaCyc: PSMD10
HUMANCyc: PSMD10
RegulationEnsembl's Regulation: ENSG00000101843
miRBase: chrX :107,327,434-107,334,874
TargetScan: NM_002814
cisRED: ENSG00000101843
ContextiHOP: PSMD10
cancer metabolism search in PubMed: PSMD10
UCL Cancer Institute: PSMD10
Assigned class in ccmGDBC

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Phenotypic Information for PSMD10(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMD10
Familial Cancer Database: PSMD10
* 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: PSMD10
MedGen: PSMD10 (Human Medical Genetics with Condition)
ClinVar: PSMD10
PhenotypeMGI: PSMD10 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMD10

Mutations for PSMD10
* 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 PSMD10 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA743558GNG41211235801786235801806PSMD1013335X107327444107327765

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
There's no copy number variation information in COSMIC data for this gene.

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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=12)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr23:107328302-107328302p.G195*3
chr23:107330981-107330981p.M154I1
chr23:107332057-107332057p.W46*1
chr23:107331000-107331000p.A148D1
chr23:107332065-107332065p.L44L1
chr23:107328209-107328209p.G226C1
chr23:107331010-107331010p.R145W1
chr23:107334727-107334727p.L8L1
chr23:107328257-107328257p.Q210*1
chr23:107331059-107331059p.G128G1

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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
# sample1 13  1    311  11 5
# mutation1 13  1    311  11 5
nonsynonymous SNV  11  1    1 1  1  4
synonymous SNV1  2       21    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
chrX:107331010p.R145W,PSMD101
chrX:107331059p.G128G,PSMD101
chrX:107328209p.H119H,PSMD101
chrX:107331186p.R118G,PSMD101
chrX:107328211p.A80V,PSMD101
chrX:107331191p.L77F,PSMD101
chrX:107328300p.N67N,PSMD101
chrX:107331304p.G226C1
chrX:107328302p.L44L,PSMD101
chrX:107331314p.E225V1

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 PSMD10 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 PSMD10

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

ATG4A,C1GALT1C1,CETN2,CUL4B,FAM199X,HPRT1,LAMP2,
MCTS1,MORF4L2,MOSPD1,NKAP,NKRF,NXT2,PRPS1,
PSMD10,TCEAL8,UBE2A,UPRT,VAMP7,VBP1,VMA21
ARV1,C18orf32,CETN2,CISD2,GGPS1,H3F3A,LOC653566,
LSM12,PIGY,POLR2K,PSMD10,SELT,SEP15,SKP1,
SPCS1,SRP9,SUMO1,SUMO2,TCEAL8,TMCO1,TMEM59

ARMCX5,C1GALT1C1,CETN2,FAM104B,FUNDC2,LAMP2,MAGT1,
MCTS1,MMGT1,MORF4L2,CMC4,NKAP,NXT2,PDZD11,
PGRMC1,PSMD10,RAP2C,RBMX2,UBE2A,VBP1,VMA21
C14orf119,C8orf59,COMMD3,DNAJC19,DPY30,GEMIN6,HAX1,
HSBP1,MRPL49,NAA20,NDUFA4,NSMCE2,OSTC,PRDX3,
PSMD10,RPL41,RPS18,RPS3A,SNRPD2,THOC7,EMC4
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 PSMD10


There's no related Drug.
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Cross referenced IDs for PSMD10
* 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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