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 NUP188

Basic gene info.	Gene symbol	NUP188
	Gene name	nucleoporin 188kDa
	Synonyms	KIAA0169\|hNup188
	Cytomap	UCSC genome browser: 9q34.11
	Genomic location	chr9 :131709976-131769374
	Type of gene	protein-coding
	RefGenes	NM_015354.2,
	Ensembl id	ENSG00000095319
	Description	nucleoporin NUP188 homolog
	Modification date	20141207
dbXrefs	MIM : 615587
	HGNC : HGNC
	Ensembl : ENSG00000095319
	HPRD : 18582
	Vega : OTTHUMG00000020768
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NUP188
	BioGPS: 23511
	Gene Expression Atlas: ENSG00000095319
	The Human Protein Atlas: ENSG00000095319
Pathway	NCI Pathway Interaction Database: NUP188
	KEGG: NUP188
	REACTOME: NUP188
	ConsensusPathDB
	Pathway Commons: NUP188
Metabolism	MetaCyc: NUP188
	HUMANCyc: NUP188
Regulation	Ensembl's Regulation: ENSG00000095319
	miRBase: chr9 :131,709,976-131,769,374
	TargetScan: NM_015354
	cisRED: ENSG00000095319
Context	iHOP: NUP188
	cancer metabolism search in PubMed: NUP188
	UCL Cancer Institute: NUP188
Assigned class in ccmGDB	C

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Phenotypic Information for NUP188(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: NUP188
	Familial Cancer Database: NUP188

* 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
Orphanet
Disease	KEGG Disease: NUP188
	MedGen: NUP188 (Human Medical Genetics with Condition)
	ClinVar: NUP188
Phenotype	MGI: NUP188 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: NUP188

Mutations for NUP188

* 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

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 NUP188 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
BE819347	NUP188	3	151	9	131768587	131768868	POLR2A	138	287	17	7407022	7411630
BE819348	NUP188	13	176	9	131768570	131768868	POLR2A	163	312	17	7407022	7411630
BG397339	NUP188	47	104	9	131769268	131769325	NUP188	100	165	9	131769308	131769373
BC071936	NUP188	22	382	9	131768366	131768976	PCNP	363	908	3	101295262	101295811
T07564	MAPK10	1	105	4	87205426	87205530	NUP188	106	293	9	131761964	131763874

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=105)	Stat. for Synonymous SNVs (# total SNVs=44)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr9:131745577-131745577	p.T601M	3
chr9:131730845-131730845	p.E216*	3
chr9:131756695-131756695	p.L1021V	2
chr9:131749122-131749122	p.L744L	2
chr9:131733044-131733044	p.D307G	2
chr9:131767960-131767960	p.L1592L	2
chr9:131745224-131745224	p.L571L	2
chr9:131750456-131750456	p.S842P	2
chr9:131730798-131730798	p.V200A	2
chr9:131763912-131763912	p.L1316L	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=6

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		20	1		4		2			19	7	5		1	11	16		16
# mutation	8	4		18	1		4		2			20	7	5		1	13	23		20
nonsynonymous SNV	6	1		15	1		3		1			13	4	3		1	6	16		13
synonymous SNV	2	3		3			1		1			7	3	2			7	7		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
chr9:131745577	p.T601M	3
chr9:131760467	p.F387F	2
chr9:131745254	p.A1666A	2
chr9:131730798	p.S581S	2
chr9:131745576	p.V200A	2
chr9:131735486	p.T601A	2
chr9:131768572	p.D307G	2
chr9:131733044	p.R1130H	2
chr9:131768878	p.L867F	1
chr9:131742903	p.S1157S	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 NUP188 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 NUP188

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


BUB1B,CAMSAP1,CKAP2L,CLSPN,DDX31,DOLPP1,EXOSC2, FANCC,GLE1,GTF3C4,LMNB1,LOC441089,NCBP1,NUP188, NUP214,NUSAP1,ODF2,POLE3,SET,SMC2,TTF1	AFAP1,ANKRD52,ARID1A,SLX4,CAD,DNMT1,DVL3, ENTPD4,LOC100129034,NEK6,NUP188,PI4KA,PLXNA1,POLR1A, RNF24,SAMD4B,SRCAP,TRRAP,UBAP2L,XPO5,XPO6

CAMSAP1,CDCA2,CDK5RAP2,CEP78,CHAF1A,CLSPN,DNMT1, FANCC,GSG2,GTF3C4,INCENP,LMNB2,MKI67,NUP188, ORC1,SEC16A,SMC2,UHRF1,WDHD1,WDR76,WHSC1	BMS1,CAD,CKAP5,ILF3,KHSRP,MDC1,NAT10, NCL,NUP188,NUP205,ODF2,PFAS,POLR1A,PRKDC, RBM19,TCHP,TCOF1,UBAP2L,URB1,UTP20,ZC3H18

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 NUP188

There's no related Drug.

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Cross referenced IDs for NUP188

* 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