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 NUP133
Basic gene info.Gene symbolNUP133
Gene namenucleoporin 133kDa
SynonymshNUP133
CytomapUCSC genome browser: 1q42.13
Genomic locationchr1 :229577043-229644088
Type of geneprotein-coding
RefGenesNM_018230.2,
Ensembl idENSG00000069248
Description133 kDa nucleoporinnuclear pore complex protein Nup133nucleoporin 133kDnucleoporin Nup133
Modification date20141207
dbXrefs MIM : 607613
HGNC : HGNC
Ensembl : ENSG00000069248
HPRD : 06354
Vega : OTTHUMG00000039462
ProteinUniProt: Q8WUM0
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NUP133
BioGPS: 55746
Gene Expression Atlas: ENSG00000069248
The Human Protein Atlas: ENSG00000069248
PathwayNCI Pathway Interaction Database: NUP133
KEGG: NUP133
REACTOME: NUP133
ConsensusPathDB
Pathway Commons: NUP133
MetabolismMetaCyc: NUP133
HUMANCyc: NUP133
RegulationEnsembl's Regulation: ENSG00000069248
miRBase: chr1 :229,577,043-229,644,088
TargetScan: NM_018230
cisRED: ENSG00000069248
ContextiHOP: NUP133
cancer metabolism search in PubMed: NUP133
UCL Cancer Institute: NUP133
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for NUP133(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NUP133
Familial Cancer Database: NUP133
* 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_NON_CODING_RNA
REACTOME_METABOLISM_OF_RNA
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 607613; gene.
Orphanet
DiseaseKEGG Disease: NUP133
MedGen: NUP133 (Human Medical Genetics with Condition)
ClinVar: NUP133
PhenotypeMGI: NUP133 (International Mouse Phenotyping Consortium)
PhenomicDB: NUP133

Mutations for NUP133
* 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 NUP133 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA418651MUSK11239113530241113530363NUP1331226161229623244229631796
AA326630SYT11218127947019579470412NUP1332113581229611451229611596
AW895718NUP1333044051229592841229593017FAF139942115140750151407526

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 # sample1         2   1  
GAIN (# sample)1         2   1  
LOSS (# sample)                 
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=77)
Stat. for Synonymous SNVs
(# total SNVs=28)
Stat. for Deletions
(# total SNVs=2)
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
chr1:229635512-229635512p.S189R3
chr1:229635521-229635521p.Y186Y3
chr1:229623211-229623211p.?3
chr1:229584922-229584922p.I1066V2
chr1:229601166-229601166p.?2
chr1:229596456-229596456p.S916P2
chr1:229631310-229631310p.G326G2
chr1:229613400-229613400p.D567G2
chr1:229622162-229622162p.L486L2
chr1:229599292-229599292p.Q895*2

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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
# sample 3 192 2 41 14931167111
# mutation 3 182 2 41 16931179112
nonsynonymous SNV 2 13  2 2  11721165110
synonymous SNV 1 52   21 521  14 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
chr1:229631744p.T290T3
chr1:229613423p.G326G2
chr1:229631310p.R559R2
chr1:229635527p.L372L1
chr1:229594020p.I233M1
chr1:229619824p.T28T1
chr1:229623332p.A1022V1
chr1:229641823p.S769N1
chr1:229600611p.L551L1
chr1:229631689p.S371Y1

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 NUP133 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 NUP133

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

ABCB10,ACBD3,ANGEL2,DIEXF,SPRTN,SDE2,BROX,
CDC73,CEP350,EXOC8,FBXO28,HEATR1,IARS2,NUP133,
RAB3GAP2,RPS6KC1,TAF1A,TAF5L,TSNAX,ZBTB41,ZNF678
API5,CDC23,CEP57,CNOT7,CTDSPL2,DDX18,DHX40,
GOSR1,GPBP1,KIAA1143,LOC144438,MATR3,NUCKS1,NUDT21,
NUP133,RAD17,RSBN1,SLC30A9,SMAD4,STAG2,TRMT5

ABCB10,ADSS,ATF6,DIEXF,SPRTN,SDE2,COG2,
HEATR1,IPO9,KLHL12,METTL13,NUP133,POGK,POLR3C,
PRUNE,RAB3GAP2,RBBP5,SETDB1,TAF5L,URB2,ZNF669
ARHGEF9,CDK5RAP2,CKAP5,DHX57,GEMIN5,INTS2,IPO9,
KIAA0586,KIAA1549,MTAP,NUP133,NUP205,PREPL,SKIV2L2,
SUPT16H,TFCP2,TMEM194A,TOP2B,TTLL5,UBAP2L,WDR82
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 NUP133


There's no related Drug.
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Cross referenced IDs for NUP133
* 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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