Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	NUP214
	Gene name	nucleoporin 214kDa
	Synonyms	CAIN\|CAN\|D9S46E\|N214\|p250
	Cytomap	UCSC genome browser: 9q34.1
	Genomic location	chr9 :134000980-134109091
	Type of gene	protein-coding
	RefGenes	NM_005085.3,
	Ensembl id	ENSG00000126883
	Description	CAN protein, putative oncogenenuclear pore complex protein Nup214
	Modification date	20141207
dbXrefs	MIM : 114350
	HGNC : HGNC
	Ensembl : ENSG00000126883
	HPRD : 00258
	Vega : OTTHUMG00000020816
Protein	UniProt: P35658 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NUP214
	BioGPS: 8021
	Gene Expression Atlas: ENSG00000126883
	The Human Protein Atlas: ENSG00000126883
Pathway	NCI Pathway Interaction Database: NUP214
	KEGG: NUP214
	REACTOME: NUP214
	ConsensusPathDB
	Pathway Commons: NUP214
Metabolism	MetaCyc: NUP214
	HUMANCyc: NUP214
Regulation	Ensembl's Regulation: ENSG00000126883
	miRBase: chr9 :134,000,980-134,109,091
	TargetScan: NM_005085
	cisRED: ENSG00000126883
Context	iHOP: NUP214
	cancer metabolism search in PubMed: NUP214
	UCL Cancer Institute: NUP214
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for NUP214(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_NON_CODING_RNA REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM	114350; gene.
Orphanet	98277; Acute myeloid leukemia with recurrent genetic anomaly.
Disease	KEGG Disease: NUP214
	MedGen: NUP214 (Human Medical Genetics with Condition)
	ClinVar: NUP214
Phenotype	MGI: NUP214 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
haematopoietic_and_lymphoid_tissue	NUP214	chr9	134099576	134099576	SQSTM1	chr5	179255575	179255575
ovary	NUP214	chr9	134098971	134099171	LINGO1	chr15	77910771	77910971

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NUP214 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BG003896	NUP214	14	72	9	134070322	134070382	INS-IGF2	67	212	11	2154279	2154423
XX000003	NOTCH1	1	59	9	139438476	139438534	NUP214	58	133	9	134062675	134062750
BF211581	NUP214	1	379	9	134074021	134074402	XKR3	377	622	22	17288733	17288976
BX487600	PRH1-PRR4	22	64	12	11084881	11084923	NUP214	59	581	9	134062501	134070726
BF082622	NUP214	10	223	9	134103618	134106129	AGGF1	224	243	5	76359022	76359041
BE837492	NUP214	17	161	9	134073077	134073222	ARHGAP26	151	341	5	142339348	142339538
BQ329628	NUP214	1	209	9	134039450	134049569	NUP214	204	279	9	134039254	134039329

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr9:134073008-134073008	p.P1378fs*3	3
chr9:134014760-134014760	p.V366V	3
chr9:134021630-134021630	p.T628T	3
chr9:134090601-134090601	p.Q1865Q	3
chr9:134034776-134034776	p.R815W	3
chr9:134073007-134073008	p.V1379fs*60	3
chr9:134039494-134039494	p.A952A	2
chr9:134026097-134026097	p.R741Q	2
chr9:134021542-134021542	p.P599L	2
chr9:134073620-134073620	p.E1580G	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	3	4	1	19	2		7		4	3		26	6	3		1	15	14	3	23
# mutation	4	4	1	21	2		9		4	3		31	6	3		1	15	20	3	28
nonsynonymous SNV	3	3	1	13	1		8		2	3		23	5	1		1	12	16	2	18
synonymous SNV	1	1		8	1		1		2			8	1	2			3	4	1	10

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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr9:134004681	p.R137C	2
chr9:134034776	p.V366V	2
chr9:134072982	p.E1580G	2
chr9:134014760	p.R815W	2
chr9:134073620	p.G1367G	2
chr9:134008519	p.G2036C	1
chr9:134098264	p.S897P	1
chr9:134022951	p.A1190T	1
chr9:134049567	p.A1392V	1
chr9:134073346	p.G549V	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA31851; -.
Organism-specific databases	CTD	8021; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00864	nucleoporin 214kDa	approved; investigational	Tacrolimus

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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