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 NUP214
Basic gene info.Gene symbolNUP214
Gene namenucleoporin 214kDa
SynonymsCAIN|CAN|D9S46E|N214|p250
CytomapUCSC genome browser: 9q34.1
Genomic locationchr9 :134000980-134109091
Type of geneprotein-coding
RefGenesNM_005085.3,
Ensembl idENSG00000126883
DescriptionCAN protein, putative oncogenenuclear pore complex protein Nup214
Modification date20141207
dbXrefs MIM : 114350
HGNC : HGNC
Ensembl : ENSG00000126883
HPRD : 00258
Vega : OTTHUMG00000020816
ProteinUniProt: P35658
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NUP214
BioGPS: 8021
Gene Expression Atlas: ENSG00000126883
The Human Protein Atlas: ENSG00000126883
PathwayNCI Pathway Interaction Database: NUP214
KEGG: NUP214
REACTOME: NUP214
ConsensusPathDB
Pathway Commons: NUP214
MetabolismMetaCyc: NUP214
HUMANCyc: NUP214
RegulationEnsembl's Regulation: ENSG00000126883
miRBase: chr9 :134,000,980-134,109,091
TargetScan: NM_005085
cisRED: ENSG00000126883
ContextiHOP: NUP214
cancer metabolism search in PubMed: NUP214
UCL Cancer Institute: NUP214
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for NUP214(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NUP214
Familial Cancer Database: NUP214
* 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_MRNA
REACTOME_METABOLISM_OF_RNA
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM 114350; gene.
Orphanet 98277; Acute myeloid leukemia with recurrent genetic anomaly.
DiseaseKEGG Disease: NUP214
MedGen: NUP214 (Human Medical Genetics with Condition)
ClinVar: NUP214
PhenotypeMGI: NUP214 (International Mouse Phenotyping Consortium)
PhenomicDB: NUP214

Mutations for NUP214
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
haematopoietic_and_lymphoid_tissueNUP214chr9134099576134099576SQSTM1chr5179255575179255575
ovaryNUP214chr9134098971134099171LINGO1chr157791077177910971
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 NUP214 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG003896NUP21414729134070322134070382INS-IGF2672121121542792154423
XX000003NOTCH11599139438476139438534NUP214581339134062675134062750
BF211581NUP21413799134074021134074402XKR3377622221728873317288976
BX487600PRH1-PRR42264121108488111084923NUP214595819134062501134070726
BF082622NUP214102239134103618134106129AGGF122424357635902276359041
BE837492NUP214171619134073077134073222ARHGAP261513415142339348142339538
BQ329628NUP21412099134039450134049569NUP2142042799134039254134039329

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=122)
Stat. for Synonymous SNVs
(# total SNVs=51)
Stat. for Deletions
(# total SNVs=7)
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
chr9:134090601-134090601p.Q1865Q3
chr9:134034776-134034776p.R815W3
chr9:134073007-134073008p.V1379fs*603
chr9:134073008-134073008p.P1378fs*33
chr9:134014760-134014760p.V366V3
chr9:134021630-134021630p.T628T3
chr9:134003761-134003761p.I95N2
chr9:134073056-134073056p.A1392V2
chr9:134020006-134020006p.S545L2
chr9:134074070-134074070p.S1730*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
# sample341192 7 43 2663 11514323
# mutation441212 9 43 3163 11520328
nonsynonymous SNV331131 8 23 2351 11216218
synonymous SNV11 81 1 2  812  34110
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
chr9:134034776p.R815W2
chr9:134072982p.G1367G2
chr9:134014760p.R137C2
chr9:134073620p.V366V2
chr9:134004681p.E1580G2
chr9:134010311p.A1632T1
chr9:134103703p.G649G1
chr9:134025762p.S1919S1
chr9:134050999p.K755N1
chr9:134073549p.S985S1

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 NUP214 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 NUP214

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

ABL1,PRRC2B,BRD3,INIP,CAMSAP1,DDX31,FKTN,
FUBP3,GLE1,GPR107,GTF3C4,KIAA0368,NUP188,NUP214,
RABGAP1,RNF20,SETX,TRIM32,TSC1,TTF1,ZBTB43
ASXL1,CNOT1,CREBBP,AGO1,EP300,EP400,MAML2,
MDC1,MDN1,MED12,MGA,KMT2A,NCOA6,NUP214,
PRPF8,SETD5,SPEN,SRRM2,TRRAP,XYLB,YLPM1

ABL1,PRRC2A,PRRC2B,BRD3,CDK5RAP2,CNTRL,CIZ1,
EHMT1,FBXW2,FUBP3,GOLGA1,KIAA0368,PPP1R26,KMT2B___KMT2D,
NUP214,RNF20,SNAPC4,TBC1D13,TSC1,UBAP2,USP20
PRRC2A,CBX5,CHERP,EP400,GCN1L1,GTF3C1,LARP1,
MTOR,NUP214,PDCD11,PRPF8,SAFB2,SAFB,SNRNP200,
SRCAP,TRRAP,UBAP2,UBE2O,YLPM1,ZC3H18,ZNF142
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 NUP214
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA31851; -.
Organism-specific databasesCTD 8021; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00864nucleoporin 214kDaapproved; investigationalTacrolimus


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Cross referenced IDs for NUP214
* 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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