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 NUP188
Basic gene info.Gene symbolNUP188
Gene namenucleoporin 188kDa
SynonymsKIAA0169|hNup188
CytomapUCSC genome browser: 9q34.11
Genomic locationchr9 :131709976-131769374
Type of geneprotein-coding
RefGenesNM_015354.2,
Ensembl idENSG00000095319
Descriptionnucleoporin NUP188 homolog
Modification date20141207
dbXrefs MIM : 615587
HGNC : HGNC
Ensembl : ENSG00000095319
HPRD : 18582
Vega : OTTHUMG00000020768
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NUP188
BioGPS: 23511
Gene Expression Atlas: ENSG00000095319
The Human Protein Atlas: ENSG00000095319
PathwayNCI Pathway Interaction Database: NUP188
KEGG: NUP188
REACTOME: NUP188
ConsensusPathDB
Pathway Commons: NUP188
MetabolismMetaCyc: NUP188
HUMANCyc: NUP188
RegulationEnsembl's Regulation: ENSG00000095319
miRBase: chr9 :131,709,976-131,769,374
TargetScan: NM_015354
cisRED: ENSG00000095319
ContextiHOP: NUP188
cancer metabolism search in PubMed: NUP188
UCL Cancer Institute: NUP188
Assigned class in ccmGDBC

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Phenotypic Information for NUP188(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_NON_CODING_RNA
REACTOME_METABOLISM_OF_RNA
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NUP188
MedGen: NUP188 (Human Medical Genetics with Condition)
ClinVar: NUP188
PhenotypeMGI: NUP188 (International Mouse Phenotyping Consortium)
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.

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
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 NUP188 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE819347NUP18831519131768587131768868POLR2A1382871774070227411630
BE819348NUP188131769131768570131768868POLR2A1633121774070227411630
BG397339NUP188471049131769268131769325NUP1881001659131769308131769373
BC071936NUP188223829131768366131768976PCNP3639083101295262101295811
T07564MAPK10110548720542687205530NUP1881062939131761964131763874

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1                
GAIN (# sample)                 
LOSS (# sample)1                
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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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=6

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check002.gifSomatic 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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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
chr9:131745577-131745577p.T601M3
chr9:131730845-131730845p.E216*3
chr9:131757790-131757790p.T1116T2
chr9:131745254-131745254p.S581S2
chr9:131735486-131735486p.F387F2
chr9:131768946-131768946p.M1747L2
chr9:131750408-131750408p.R826G2
chr9:131760467-131760467p.R1130H2
chr9:131750420-131750420p.P830S2
chr9:131745645-131745645p.R624S2

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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=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample84 201 4 2  1975 11116 16
# mutation84 181 4 2  2075 11323 20
nonsynonymous SNV61 151 3 1  1343 1616 13
synonymous SNV23 3  1 1  732  77 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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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
chr9:131745577p.T601M3
chr9:131735486p.F387F2
chr9:131768572p.A1666A2
chr9:131733044p.S581S2
chr9:131760467p.V200A2
chr9:131745254p.T601A2
chr9:131730798p.D307G2
chr9:131745576p.R1130H2
chr9:131768567p.A840V1
chr9:131747191p.D1135D1

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 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

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

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
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 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



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