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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 NUP85

Basic gene info.	Gene symbol	NUP85
	Gene name	nucleoporin 85kDa
	Synonyms	Nup75
	Cytomap	UCSC genome browser: 17q25.1
	Genomic location	chr17 :73201596-73231854
	Type of gene	protein-coding
	RefGenes	NM_024844.3,
	Ensembl id	ENSG00000125450
	Description	85 kDa nucleoporinfrountnuclear pore complex protein Nup85nucleoporin Nup75nucleoporin Nup85pericentrin-1
	Modification date	20141207
dbXrefs	MIM : 170285
	HGNC : HGNC
	Ensembl : ENSG00000125450
	HPRD : 01363
	Vega : OTTHUMG00000179482
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NUP85
	BioGPS: 79902
	Gene Expression Atlas: ENSG00000125450
	The Human Protein Atlas: ENSG00000125450
Pathway	NCI Pathway Interaction Database: NUP85
	KEGG: NUP85
	REACTOME: NUP85
	ConsensusPathDB
	Pathway Commons: NUP85
Metabolism	MetaCyc: NUP85
	HUMANCyc: NUP85
Regulation	Ensembl's Regulation: ENSG00000125450
	miRBase: chr17 :73,201,596-73,231,854
	TargetScan: NM_024844
	cisRED: ENSG00000125450
Context	iHOP: NUP85
	cancer metabolism search in PubMed: NUP85
	UCL Cancer Institute: NUP85
Assigned class in ccmGDB	C

Top

Phenotypic Information for NUP85(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: NUP85
	Familial Cancer Database: NUP85

* 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: NUP85
	MedGen: NUP85 (Human Medical Genetics with Condition)
	ClinVar: NUP85
Phenotype	MGI: NUP85 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: NUP85

Mutations for NUP85

* 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 NUP85 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
DB001249	WBP2	3	204	17	73847647	73851410	NUP85	194	564	17	73211843	73221471
DA567594	ZNF77	1	418	19	2936522	2944945	NUP85	417	535	17	73208085	73209216
CA313471	NUP85	18	123	17	73231748	73231853	NUP85	111	190	17	73231707	73231786
CB243613	NUP85	18	123	17	73231748	73231853	NUP85	111	190	17	73231707	73231786
AA593414	NUP85	1	235	17	73227200	73227434	NUP85	226	349	17	73229033	73229156

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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=2

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=30)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

Top

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
chr17:73231708-73231708	p.L635L	2
chr17:73231715-73231715	p.S638P	2
chr17:73222233-73222233	p.Q359*	2
chr17:73231731-73231731	p.L643H	2
chr17:73227439-73227439	p.A367T	2
chr17:73221509-73221509	p.L269I	2
chr17:73209205-73209205	p.F132F	2
chr17:73221904-73221904	p.D323N	1
chr17:73231686-73231686	p.E628G	1
chr17:73204717-73204717	p.?	1

Top

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	6			9			2		1			5	1	2			7	7		6
# mutation	6			7			2		1			5	2	2			7	7		7
nonsynonymous SNV	4			5			1		1			4	1	2			4	6		7
synonymous SNV	2			2			1					1	1				3	1

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])

Top

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
chr17:73227439	p.A367T	3
chr17:73228951	p.E114D	1
chr17:73208107	p.F411L	1
chr17:73230872	p.E620K	1
chr17:73221904	p.E155D	1
chr17:73228962	p.R460L	1
chr17:73208116	p.L622F	1
chr17:73231231	p.L163L	1
chr17:73222188	p.S468G	1
chr17:73228981	p.D626N	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 NUP85 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]

Top

Gene Expression for NUP85

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


ATP5H,BIRC5,METTL23,GGA3,HN1,ICT1,JMJD6, LLGL2,MRPL38,MRPS7,NAT9,NUP85,RECQL5,SAP30BP, SRSF2,SLC25A19,SUMO2,ALYREF,TMEM104,TSEN54,UBE2O	ACD,TMEM234,CCDC84,DDX39A,DEF6,EGFL8,LAT, LUC7L,NFKBIE,NUP85,PABPN1,PBX4,POLR2H,PRR14, RHBDF2,SDCCAG3,SNHG12,TMEM86B,TNFRSF14,TOR2A,ZGLP1

ATP5H,BIRC5,C17orf53,CCDC137,EFTUD2,EIF4A3,ERAL1, ICT1,MRPL12,MRPL38,MRPS7,NAT9,NME1,NUP85, PHB,SRSF2,SLC25A19,TACO1,ALYREF,TSEN54,UTP18	BIRC5,DDIAS,CDCA4,CDK1,CHEK2,DBF4,DNAJC9, DSN1,DTYMK,GINS1,GINS2,KIAA0101,NUP85,ORC6, PCNA,POLE2,PYCR1,RAD51AP1,RANBP1,UBE2T,UTP6

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for NUP85

There's no related Drug.

Top

Cross referenced IDs for NUP85

* 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