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 PSMD13
Basic gene info.Gene symbolPSMD13
Gene nameproteasome (prosome, macropain) 26S subunit, non-ATPase, 13
SynonymsHSPC027|Rpn9|S11|p40.5
CytomapUCSC genome browser: 11p15.5
Genomic locationchr11 :236807-252984
Type of geneprotein-coding
RefGenesNM_002817.3,
NM_175932.2,
Ensembl idENSG00000185627
Description26S proteasome non-ATPase regulatory subunit 1326S proteasome regulatory subunit RPN926S proteasome regulatory subunit S1126S proteasome regulatory subunit p40.526S proteasome subunit p40.5
Modification date20141207
dbXrefs MIM : 603481
HGNC : HGNC
Ensembl : ENSG00000185627
HPRD : 04595
Vega : OTTHUMG00000119072
ProteinUniProt: Q9UNM6
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMD13
BioGPS: 5719
Gene Expression Atlas: ENSG00000185627
The Human Protein Atlas: ENSG00000185627
PathwayNCI Pathway Interaction Database: PSMD13
KEGG: PSMD13
REACTOME: PSMD13
ConsensusPathDB
Pathway Commons: PSMD13
MetabolismMetaCyc: PSMD13
HUMANCyc: PSMD13
RegulationEnsembl's Regulation: ENSG00000185627
miRBase: chr11 :236,807-252,984
TargetScan: NM_002817
cisRED: ENSG00000185627
ContextiHOP: PSMD13
cancer metabolism search in PubMed: PSMD13
UCL Cancer Institute: PSMD13
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PSMD13(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMD13
Familial Cancer Database: PSMD13
* 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 603481; gene.
Orphanet
DiseaseKEGG Disease: PSMD13
MedGen: PSMD13 (Human Medical Genetics with Condition)
ClinVar: PSMD13
PhenotypeMGI: PSMD13 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMD13

Mutations for PSMD13
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPSMD13chr11237770237790chr162151828521518305
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 PSMD13 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BX103504PSMD13140111237045244761FAM157B4004939141131447141131540
BF768948EIF3D2312223691489136916733PSMD1330340411252820252921

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=5

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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=14)
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
chr11:244167-244167p.N72N5
chr11:237087-237087p.N13S4
chr11:247370-247370p.Q164K3
chr11:244428-244428p.P90S2
chr11:250827-250827p.Q267*2
chr11:247372-247372p.Q164Q2
chr11:244171-244171p.L74L2
chr11:248825-248825p.L206L1
chr11:251630-251630p.?1
chr11:244197-244197p.H82H1

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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 119    2  311  32 1
# mutation 118    2  411  22 2
nonsynonymous SNV   6       311  22 1
synonymous SNV 112    2  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
chr11:247370p.Q166K,PSMD133
chr11:247372p.N74N,PSMD132
chr11:244167p.P92S,PSMD132
chr11:244428p.Q166Q,PSMD132
chr11:251916p.T38A1
chr11:252523p.H334Y,PSMD131
chr11:252542p.P48L1
chr11:248825p.R341R,PSMD131
chr11:252595p.I58T1
chr11:237137p.R354S,PSMD131

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 PSMD13 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 PSMD13

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

LBHD1___C11orf98,HRAS,MOB2,MRPL17,MRPL23,NDUFA11,NDUFS3,
PEX16,PKP3,PRDX5,PSMB6,PSMC3,PSMD13,PTDSS2,
RHOG,RPL27A,RPLP2,SURF2,TAF10,TALDO1,TSSC4
ASNA1,ELP6,CHMP2A,FAM58A,MRPL28,MRPL51,MRPS34,
NUDC,PFDN6,PMF1,PMVK,POLR2F,POP7,PPP1CA,
PSMC5,PSMD13,RAB1B,RNF187,SNRNP35,UBE2J2,WBSCR22

ATP5L,BANF1,EMG1,GADD45GIP1,LSM4,MRPL11,MRPL17,
MRPL23,NDUFS3,PSMA1,PSMB1,PSMB3,PSMB4,PSMC3,
PSMD13,PTPMT1,RNF181,SDHAF2,MSRB1,TALDO1,PAM16
SLIRP,EMC7,DAD1,LSM1,MRPL20,PGK1,POMP,
PSMA1,PSMA2,PSMA5,PSMA6,PSMA7,PSMB1,PSMB4,
PSMC6,PSMD13,PSMD8,PTS,RBX1,STRA13,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 PSMD13


There's no related Drug.
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Cross referenced IDs for PSMD13
* 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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