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 NUP153
Basic gene info.Gene symbolNUP153
Gene namenucleoporin 153kDa
SynonymsHNUP153|N153
CytomapUCSC genome browser: 6p22.3
Genomic locationchr6 :17615268-17706818
Type of geneprotein-coding
RefGenesNM_001278209.1,
NM_001278210.1,NM_005124.3,
Ensembl idENSG00000124789
Description153 kDa nucleoporinnuclear pore complex protein Nup153nuclear pore complex protein hnup153nucleoporin 153kDnucleoporin Nup153
Modification date20141207
dbXrefs MIM : 603948
HGNC : HGNC
Ensembl : ENSG00000124789
HPRD : 04899
Vega : OTTHUMG00000014312
ProteinUniProt: P49790
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NUP153
BioGPS: 9972
Gene Expression Atlas: ENSG00000124789
The Human Protein Atlas: ENSG00000124789
PathwayNCI Pathway Interaction Database: NUP153
KEGG: NUP153
REACTOME: NUP153
ConsensusPathDB
Pathway Commons: NUP153
MetabolismMetaCyc: NUP153
HUMANCyc: NUP153
RegulationEnsembl's Regulation: ENSG00000124789
miRBase: chr6 :17,615,268-17,706,818
TargetScan: NM_001278209
cisRED: ENSG00000124789
ContextiHOP: NUP153
cancer metabolism search in PubMed: NUP153
UCL Cancer Institute: NUP153
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for NUP153(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NUP153
Familial Cancer Database: NUP153
* 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 603948; gene.
Orphanet
DiseaseKEGG Disease: NUP153
MedGen: NUP153 (Human Medical Genetics with Condition)
ClinVar: NUP153
PhenotypeMGI: NUP153 (International Mouse Phenotyping Consortium)
PhenomicDB: NUP153

Mutations for NUP153
* 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
ovaryNUP153chr61764887217648892NUP153chr61765068017650700
ovaryNUP153chr61765126917651289ICKchr65291952452919544
ovaryNUP153chr61768663417686654NUP153chr61763666417636684
pancreasNUP153chr61767323617673256chr62775226527752285
pancreasNUP153chr61770073717700757NUP153chr61770289717702917
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 NUP153 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP352751NUP153130761762479117626071NUP15330754361764803817649531
AA281956NUP153911361766546917665573NUP15310044861766972817675782

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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=99)
Stat. for Synonymous SNVs
(# total SNVs=29)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr6:17637424-17637424p.A808A4
chr6:17629357-17629357p.G1025S3
chr6:17629745-17629745p.S895S3
chr6:17637996-17637996p.A618T3
chr6:17669558-17669558p.R327K2
chr6:17629507-17629507p.D975Y2
chr6:17637577-17637577p.A757A2
chr6:17675874-17675874p.S154S2
chr6:17629253-17629253p.S1059S2
chr6:17629625-17629625p.G935G2

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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
# sample461132 5 61 992  716 14
# mutation461122 5 61 9102  817 22
nonsynonymous SNV35182 4 41 872  613 17
synonymous SNV11 4  1 2  13   24 5
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
chr6:17637604p.A589T,NUP1533
chr6:17637957p.P706P,NUP1533
chr6:17629253p.F939C,NUP1532
chr6:17675207p.A576T,NUP1532
chr6:17629625p.G893G,NUP1532
chr6:17629745p.S853S,NUP1532
chr6:17629488p.S1017S,NUP1532
chr6:17637996p.P261T,NUP1532
chr6:17637557p.G4E,NUP1531
chr6:17669558p.S989A,NUP1531

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 NUP153 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 NUP153

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

MMS22L,DEK,DHX9,E2F3,FAM8A1,GAS2L3,KCTD20,
KDM1B,LOC221710,NUP153,NUP155,NUP160,PRPF4B,RIF1,
SLC30A6,STRN,TET3,USP34,XPO1,ZFR,ZNF184
AFF4,BCLAF1,TRAPPC11,JMJD1C,KIAA2026,LATS1,MAP3K7,
NUP153,NUP98,RANBP2,SCAF8,RBM27,RIF1,RLF,
LTN1,RNF169,SON,SRFBP1,WAPAL,ZBTB11,ZNF644

ANKS1A,PRRC2A,CDYL,DEK,DHX16,E2F3,JARID2,
KDM1B,LATS1,MDC1,MDN1,NUP153,PRPF4B,RBM12,
SCAF8,RIF1,SHPRH,UHRF1BP1,XPO5,ZKSCAN8,ZNF318
AQR,PRRC2C,BCLAF1,CDK12,CHD7,E2F3,OTULIN,
IQGAP1,NFKB1,NUP153,RALGAPA1,SAFB,SART3,SF3B3,
SFPQ,SCAF4,UBAP2,UGGT1,USP24,VPRBP,WAPAL
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 NUP153


There's no related Drug.
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Cross referenced IDs for NUP153
* 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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