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 NUP210
Basic gene info.Gene symbolNUP210
Gene namenucleoporin 210kDa
SynonymsGP210|POM210
CytomapUCSC genome browser: 3p25.1
Genomic locationchr3 :13357736-13461809
Type of geneprotein-coding
RefGenesNM_024923.3,
Ensembl idENSG00000132182
Descriptionnuclear envelope pore membrane protein POM 210nuclear pore membrane glycoprotein 210nuclear pore protein gp210nucleoporin Nup210pore membrane protein of 210 kDa
Modification date20141207
dbXrefs MIM : 607703
HGNC : HGNC
Ensembl : ENSG00000132182
HPRD : 06368
Vega : OTTHUMG00000157268
ProteinUniProt: Q8TEM1
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NUP210
BioGPS: 23225
Gene Expression Atlas: ENSG00000132182
The Human Protein Atlas: ENSG00000132182
PathwayNCI Pathway Interaction Database: NUP210
KEGG: NUP210
REACTOME: NUP210
ConsensusPathDB
Pathway Commons: NUP210
MetabolismMetaCyc: NUP210
HUMANCyc: NUP210
RegulationEnsembl's Regulation: ENSG00000132182
miRBase: chr3 :13,357,736-13,461,809
TargetScan: NM_024923
cisRED: ENSG00000132182
ContextiHOP: NUP210
cancer metabolism search in PubMed: NUP210
UCL Cancer Institute: NUP210
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for NUP210(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NUP210
Familial Cancer Database: NUP210
* 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 607703; gene.
Orphanet
DiseaseKEGG Disease: NUP210
MedGen: NUP210 (Human Medical Genetics with Condition)
ClinVar: NUP210
PhenotypeMGI: NUP210 (International Mouse Phenotyping Consortium)
PhenomicDB: NUP210

Mutations for NUP210
* 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 NUP210 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW801070SURF29719136226834136226896NUP2105715931339018513390287
AW800948SURF211789136226834136226901NUP2105916131339018513390287
AW867470MALAT11401116526827365268673NUP21039954331336738113368810
BF814512NUP2104148731339324713395161RPS4X486544X7149376671493824
BF331537NUP2101311531339281913392920FBXO410731754192616041926370
BE073326NUP210611431339281113392920FBXO410631654192616041926370
BE073423NUP210311031339281313392920FBXO410231254192616041926370
BI047863CASP10352152202082858202083038NUP21020227131337200213372071

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 # sample2  1            3
GAIN (# sample)1  1            3
LOSS (# sample)1                
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=129)
Stat. for Synonymous SNVs
(# total SNVs=44)
Stat. for Deletions
(# total SNVs=3)
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
chr3:13417924-13417924p.R387Q4
chr3:13376971-13376971p.D1276N3
chr3:13395078-13395078p.L868L3
chr3:13378289-13378289p.E1228K3
chr3:13421116-13421116p.S308L2
chr3:13401869-13401869p.E685E2
chr3:13438914-13438914p.E127K2
chr3:13383322-13383322p.G1052S2
chr3:13384688-13384688p.R984H2
chr3:13364912-13364912p.Q1555Q2

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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
# sample84 213 5 21 1648 13716 18
# mutation104 273 5 21 1758 14520 20
nonsynonymous SNV42 182 3 21 1536 12911 13
synonymous SNV62 91 2    222  169 7
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
chr3:13417924p.R387Q3
chr3:13378289p.E1228K3
chr3:13363298p.T1651T2
chr3:13393384p.I1133I2
chr3:13381426p.A944T2
chr3:13417095p.E447V2
chr3:13363131p.P1080P1
chr3:13421065p.S1886F1
chr3:13372064p.P768T1
chr3:13381436p.G596E1

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 NUP210 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 NUP210

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

CKAP2L,CLSPN,CNOT10,FANCD2,FANCI,FOXM1,KIF15,
KIF4A,MCM2,MKI67,MSH6,NCAPG2,NUP210,POLQ,
RAD18,RAF1,SETD5,SGOL1,TATDN2,TOPBP1,WDR76
ARNT2,DNMT1,ESRP1,EZH2,FANCD2,FBXO41,ISG20L2,
JARID2,KIF24,MCM4,MEX3A,MYO19,MYO5B,NUP210,
PASK,SPATS2,STIL,STRBP,TTLL4,VANGL2,ZBED4

BUB1,CDCA5,CENPO,CHAF1A,CLSPN,DHX30,DNMT1,
E2F7,EXO1,FEN1,GSG2,GTSE1,HNRNPM,INCENP,
LMNB2,MCM10,MCM2,NCAPH,NUP210,UHRF1,WHSC1
AKNA,BEND4,CARD11,DOCK2,DOCK8,DOK3,IKZF1,
IKZF3,INPP5D,MAP4K1,NUP210,P2RY8,POU2AF1,RASSF5,
RLTPR,SEMA4A,SEMA4D,SP140,SYVN1,WDFY4,ZNF831
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 NUP210


There's no related Drug.
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Cross referenced IDs for NUP210
* 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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