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 NUP210

Basic gene info.	Gene symbol	NUP210
	Gene name	nucleoporin 210kDa
	Synonyms	GP210\|POM210
	Cytomap	UCSC genome browser: 3p25.1
	Genomic location	chr3 :13357736-13461809
	Type of gene	protein-coding
	RefGenes	NM_024923.3,
	Ensembl id	ENSG00000132182
	Description	nuclear envelope pore membrane protein POM 210nuclear pore membrane glycoprotein 210nuclear pore protein gp210nucleoporin Nup210pore membrane protein of 210 kDa
	Modification date	20141207
dbXrefs	MIM : 607703
	HGNC : HGNC
	Ensembl : ENSG00000132182
	HPRD : 06368
	Vega : OTTHUMG00000157268
Protein	UniProt: Q8TEM1 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NUP210
	BioGPS: 23225
	Gene Expression Atlas: ENSG00000132182
	The Human Protein Atlas: ENSG00000132182
Pathway	NCI Pathway Interaction Database: NUP210
	KEGG: NUP210
	REACTOME: NUP210
	ConsensusPathDB
	Pathway Commons: NUP210
Metabolism	MetaCyc: NUP210
	HUMANCyc: NUP210
Regulation	Ensembl's Regulation: ENSG00000132182
	miRBase: chr3 :13,357,736-13,461,809
	TargetScan: NM_024923
	cisRED: ENSG00000132182
Context	iHOP: NUP210
	cancer metabolism search in PubMed: NUP210
	UCL Cancer Institute: NUP210
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for NUP210(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_NON_CODING_RNA REACTOME_METABOLISM_OF_RNA REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM	607703; gene.
Orphanet
Disease	KEGG Disease: NUP210
	MedGen: NUP210 (Human Medical Genetics with Condition)
	ClinVar: NUP210
Phenotype	MGI: NUP210 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NUP210 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
AW801070	SURF2	9	71	9	136226834	136226896	NUP210	57	159	3	13390185	13390287
AW800948	SURF2	11	78	9	136226834	136226901	NUP210	59	161	3	13390185	13390287
AW867470	MALAT1	1	401	11	65268273	65268673	NUP210	399	543	3	13367381	13368810
BF814512	NUP210	41	487	3	13393247	13395161	RPS4X	486	544	X	71493766	71493824
BF331537	NUP210	13	115	3	13392819	13392920	FBXO4	107	317	5	41926160	41926370
BE073326	NUP210	6	114	3	13392811	13392920	FBXO4	106	316	5	41926160	41926370
BE073423	NUP210	3	110	3	13392813	13392920	FBXO4	102	312	5	41926160	41926370
BI047863	CASP10	35	215	2	202082858	202083038	NUP210	202	271	3	13372002	13372071

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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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=4

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Somatic 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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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
chr3:13417924-13417924	p.R387Q	4
chr3:13378289-13378289	p.E1228K	3
chr3:13376971-13376971	p.D1276N	3
chr3:13395078-13395078	p.L868L	3
chr3:13371956-13371956	p.?	2
chr3:13372109-13372109	p.R1321C	2
chr3:13381524-13381524	p.E1101K	2
chr3:13371977-13371977	p.I1365L	2
chr3:13381378-13381378	p.T1149T	2
chr3:13368892-13368892	p.C1444C	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	8	4		21	3		5		2	1		16	4	8		1	37	16		18
# mutation	10	4		27	3		5		2	1		17	5	8		1	45	20		20
nonsynonymous SNV	4	2		18	2		3		2	1		15	3	6		1	29	11		13
synonymous SNV	6	2		9	1		2					2	2	2			16	9		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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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
chr3:13378289	p.E1228K	3
chr3:13417924	p.R387Q	3
chr3:13363298	p.I1133I	2
chr3:13393384	p.A944T	2
chr3:13381426	p.E447V	2
chr3:13417095	p.T1651T	2
chr3:13368919	p.F511V	1
chr3:13441258	p.S1375S	1
chr3:13379373	p.N337S	1
chr3:13401854	p.T1251A	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 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

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


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

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 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