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 PSMD1
Basic gene info.Gene symbolPSMD1
Gene nameproteasome (prosome, macropain) 26S subunit, non-ATPase, 1
SynonymsP112|Rpn2|S1
CytomapUCSC genome browser: 2q37.1
Genomic locationchr2 :231921577-232037540
Type of geneprotein-coding
RefGenesNM_001191037.1,
NM_002807.3,NR_034059.1,
Ensembl idENSG00000173692
Description26S proteasome non-ATPase regulatory subunit 126S proteasome regulatory subunit RPN226S proteasome regulatory subunit S126S proteasome subunit p112
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000173692
HPRD : 10169
Vega : OTTHUMG00000133223
ProteinUniProt: Q99460
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSMD1
BioGPS: 5707
Gene Expression Atlas: ENSG00000173692
The Human Protein Atlas: ENSG00000173692
PathwayNCI Pathway Interaction Database: PSMD1
KEGG: PSMD1
REACTOME: PSMD1
ConsensusPathDB
Pathway Commons: PSMD1
MetabolismMetaCyc: PSMD1
HUMANCyc: PSMD1
RegulationEnsembl's Regulation: ENSG00000173692
miRBase: chr2 :231,921,577-232,037,540
TargetScan: NM_001191037
cisRED: ENSG00000173692
ContextiHOP: PSMD1
cancer metabolism search in PubMed: PSMD1
UCL Cancer Institute: PSMD1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PSMD1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PSMD1
Familial Cancer Database: PSMD1
* 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: PSMD1
MedGen: PSMD1 (Human Medical Genetics with Condition)
ClinVar: PSMD1
PhenotypeMGI: PSMD1 (International Mouse Phenotyping Consortium)
PhenomicDB: PSMD1

Mutations for PSMD1
* 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
ovaryPSMD1chr2231931976231931996PSMD1chr2231953437231953457
ovaryPSMD1chr2232030759232030779HTR2Bchr2231973346231973366
pancreasPSMD1chr2231923765231923785PSMD1chr2231923823231923843
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 PSMD1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE769099TRIM2620297614452161445492PSMD12903842232035509232035604
DA454373PSMD113222232029976232035428PSMD13195722231927240231931723
BU730843ATP2B318272X152835166152835420PSMD12707552232030589232037436

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=60)
Stat. for Synonymous SNVs
(# total SNVs=20)
Stat. for Deletions
(# total SNVs=4)
Stat. for Insertions
(# total SNVs=3)

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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
chr2:231943447-231943447p.S382S2
chr2:231927025-231927025p.V42I2
chr2:231949808-231949808p.R600*2
chr2:231931680-231931680p.K124fs*112
chr2:231937097-231937097p.N283N2
chr2:232035319-232035319p.E919K2
chr2:232035369-232035369p.I935I2
chr2:231934886-231934886p.?2
chr2:231944984-231944984p.I457V2
chr2:231948391-231948391p.R546C2

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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
# sample23 13  2 4  361  64 8
# mutation23 17  2 4  361  84 11
nonsynonymous SNV23 13  1 1  341  54 9
synonymous SNV   4  1 3   2   3  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
chr2:232035369p.R546C,PSMD12
chr2:231948391p.I904I,PSMD12
chr2:232035319p.S263S,PSMD11
chr2:231940241p.D495N,PSMD11
chr2:231947666p.V761F,PSMD11
chr2:231927224p.V47I,PSMD11
chr2:232010954p.T284M,PSMD11
chr2:231934808p.L496V,PSMD11
chr2:231941799p.N805S1
chr2:231947669p.Y49Y,PSMD11

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 PSMD1 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 PSMD1

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

KNSTRN,MTFR2,FARSB,KCMF1,KPNA2,NCAPG,NOP58,
OIP5,ORC6,PNO1,PSMA3,PSMA4,PSMB2,PSMC2,
PSMD14,PSMD1,RRM2,SNRPG,SPC25,SSB,ZC3H15
ANXA7,ATG4A,BOLA3,C20orf24,FAM98A,GTF3A,GTF3C6,
LDHA,MTCH2,PGK1,PRPS1,PSMA3,PSMC2,PSMD14,
PSMD1,PSMD6,PSMD7,TIMM17A,TTC1,UBE2F,WSB2

CCT4,GLRX3,HSPE1,MEMO1,MRPL44,MRPS23,MYEOV2,
NIF3L1,NME1,OLA1,ORC4,PNO1,PSMA1,PSMB1,
PSMD14,SRSF3,SRSF7,SNRPG,SUMO1,WDR12,YWHAQ
EBNA1BP2,EIF5AL1,HAT1,HSPE1,MAGOHB,NME1,PPIL1,
PSMA1,PSMA5,PSMA7,PSMC6,PSMD14,PSMD6,RAN,
RPL26L1,SNRPD1,SNRPG,SSBP1,TCEB1,TOMM5,UBE2N
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 PSMD1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA33899; -.
Organism-specific databasesPharmGKB PA33899; -.
Organism-specific databasesCTD 5707; -.
Organism-specific databasesCTD 5707; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00188proteasome (prosome, macropain) 26S subunit, non-ATPase, 1approved; investigationalBortezomib


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Cross referenced IDs for PSMD1
* 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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