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 NUP43
Basic gene info.Gene symbolNUP43
Gene namenucleoporin 43kDa
SynonymsbA350J20.1|p42
CytomapUCSC genome browser: 6q25.1
Genomic locationchr6 :150045456-150067688
Type of geneprotein-coding
RefGenesNM_024647.4,
NM_198887.2,NR_104456.1,
Ensembl idENSG00000120253
Descriptionnucleoporin Nup43nup107-160 subcomplex subunit Nup43
Modification date20141207
dbXrefs MIM : 608141
HGNC : HGNC
Ensembl : ENSG00000120253
HPRD : 12174
Vega : OTTHUMG00000015795
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NUP43
BioGPS: 348995
Gene Expression Atlas: ENSG00000120253
The Human Protein Atlas: ENSG00000120253
PathwayNCI Pathway Interaction Database: NUP43
KEGG: NUP43
REACTOME: NUP43
ConsensusPathDB
Pathway Commons: NUP43
MetabolismMetaCyc: NUP43
HUMANCyc: NUP43
RegulationEnsembl's Regulation: ENSG00000120253
miRBase: chr6 :150,045,456-150,067,688
TargetScan: NM_024647
cisRED: ENSG00000120253
ContextiHOP: NUP43
cancer metabolism search in PubMed: NUP43
UCL Cancer Institute: NUP43
Assigned class in ccmGDBC

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Phenotypic Information for NUP43(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NUP43
Familial Cancer Database: NUP43
* 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
Orphanet
DiseaseKEGG Disease: NUP43
MedGen: NUP43 (Human Medical Genetics with Condition)
ClinVar: NUP43
PhenotypeMGI: NUP43 (International Mouse Phenotyping Consortium)
PhenomicDB: NUP43

Mutations for NUP43
* 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 NUP43 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=27)
Stat. for Synonymous SNVs
(# total SNVs=1)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr6:150067096-150067096p.G75C2
chr6:150063525-150063525p.?1
chr6:150067090-150067090p.V77L1
chr6:150048189-150048189p.V353V1
chr6:150057671-150057671p.L242F1
chr6:150063573-150063573p.R152Q1
chr6:150048203-150048203p.R349W1
chr6:150057682-150057682p.D239H1
chr6:150063595-150063595p.V145I1
chr6:150067104-150067104p.R72T1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample3  2  2    71  122 3
# mutation3  2  2    71  122 3
nonsynonymous SNV2  2  2    71  112 2
synonymous SNV1               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
chr6:150048232p.N106I1
chr6:150063573p.R339Q1
chr6:150048281p.G75C1
chr6:150063595p.H323Y1
chr6:150052833p.R72T1
chr6:150063596p.L277V1
chr6:150052870p.D64E1
chr6:150063650p.M264I1
chr6:150057671p.M1I1
chr6:150064774p.L242F1

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 NUP43 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 NUP43

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

BCLAF1,GINM1,FBXO30,FBXO5,KATNA1,LATS1,LRP11,
LTV1,MTRF1L,NUP43,ORC3,PCMT1,PEX3,PPIL4,
SCAF8,SENP6,SHPRH,SNX14,TAB2,VTA1,ZBTB2
C17orf75,CBR4,CNOT6,ETNK1,MTF2,NUP43,PDIK1L,
SLC11A2,TIA1,TMEM41B,ZBED5,ZNF260,ZNF273,ZNF439,
ZNF443,ZNF461,ZNF493,ZNF529,ZNF708,ZNF709,ZNF738

MTFR2,FBXO5,FGFR1OP,HBS1L,HDAC2,LTV1,MAP7,
MRPL18,MRS2,NUP43,ORC3,PCMT1,PDCD2,QRSL1,
RFC4,TBP,TCP1,TFB1M,TRMT11,TTK,ZUFSP
CEP83,FKTN,G2E3,HN1L,L2HGDH,MMACHC,MRPS25,
MYB,NR2C1,NSUN4,NUP43,PTCD3,SHQ1,SRPK1,
THOC1,TMEM168,TTPA,UNG,WDR89,ZNF138,ZNF28
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 NUP43


There's no related Drug.
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Cross referenced IDs for NUP43
* 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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