Cancer Cell Metabolism Gene Database

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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 NUP107
Basic gene info.Gene symbolNUP107
Gene namenucleoporin 107kDa
SynonymsNUP84
CytomapUCSC genome browser: 12q15
Genomic locationchr12 :69080730-69136473
Type of geneprotein-coding
RefGenesNM_020401.2,
Ensembl idENSG00000111581
Description107 kDa nucleoporinnuclear pore complex protein Nup107nucleoporin Nup107
Modification date20141207
dbXrefs MIM : 607617
HGNC : HGNC
Ensembl : ENSG00000111581
HPRD : 06356
Vega : OTTHUMG00000169265
ProteinUniProt: P57740
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NUP107
BioGPS: 57122
Gene Expression Atlas: ENSG00000111581
The Human Protein Atlas: ENSG00000111581
PathwayNCI Pathway Interaction Database: NUP107
KEGG: NUP107
REACTOME: NUP107
ConsensusPathDB
Pathway Commons: NUP107
MetabolismMetaCyc: NUP107
HUMANCyc: NUP107
RegulationEnsembl's Regulation: ENSG00000111581
miRBase: chr12 :69,080,730-69,136,473
TargetScan: NM_020401
cisRED: ENSG00000111581
ContextiHOP: NUP107
cancer metabolism search in PubMed: NUP107
UCL Cancer Institute: NUP107
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for NUP107(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NUP107
Familial Cancer Database: NUP107
* 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 607617; gene.
Orphanet
DiseaseKEGG Disease: NUP107
MedGen: NUP107 (Human Medical Genetics with Condition)
ClinVar: NUP107
PhenotypeMGI: NUP107 (International Mouse Phenotyping Consortium)
PhenomicDB: NUP107

Mutations for NUP107
* 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
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryNUP107chr126911971469119734chr127053881070538830
pancreasNUP107chr126912409169124111chr11127583070127583090
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 NUP107 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI445956SEC23A28117143956026539560358NUP107116140126908394169083966

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 # sample616      2 1  21 1
GAIN (# sample)616      2 1  21 1
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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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=74)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted 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
chr12:69120309-69120309p.S536F2
chr12:69125034-69125034p.E627K2
chr12:69083345-69083345p.T45A2
chr12:69120344-69120344p.R548C2
chr12:69090606-69090606p.M152I2
chr12:69084465-69084465p.G81E2
chr12:69084481-69084481p.S86S2
chr12:69082779-69082779p.E16K2
chr12:69094533-69094533p.R194*2
chr12:69085800-69085801p.S119>?1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample551124 2 3  1021 2610 11
# mutation551145 2 3  1221 2611 14
nonsynonymous SNV441135 1 2  1021 169 12
synonymous SNV11 1  1 1  2   1 2 2
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
chr12:69083345p.P855S2
chr12:69082777p.T863M2
chr12:69135653p.R15Q2
chr12:69135678p.T45A2
chr12:69090644p.T45N1
chr12:69121157p.R264Q1
chr12:69135710p.L431S1
chr12:69107539p.E627K1
chr12:69126423p.M767I1
chr12:69113358p.R54Q1

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 NUP107 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 NUP107

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

ARHGEF18,SMIM24,CAND1,CCT2,CNOT2,CPSF6,DYRK2,
FRS2,LEMD3,LOC100128573,MDM1,MDM2,NUP107,RAB21,
RAB3IP,RAP1B,SLC35E3,TBC1D15,TMEM19,YEATS4,ZNF557
CAND1,CCDC60,CNOT2,CPSF6,DCAF10,ELAVL3,FRS2,
GRIP1,HELB,LMLN,LOC653544,MDM1,MDM2,NUP107,
OR4F17,PUS7L,UTP15,VPS35,ZFC3H1,ZMYM2,ZNF440

ANAPC7,DDIAS,TICRR,CEP83,CCT2,CDK2,CPSF6,
DDX55,DENR,FANCB,KIF23,KNTC1,NEDD1,NUP107,
NUP37,ORC6,PA2G4,RACGAP1,SNRPF,TMEM194A,TROAP
ATAD2,BRCA1,CSE1L,FANCB,FANCM,FIGNL1,HAUS6,
HNRNPR,IARS,MCM3,MTBP,NASP,NUP107,NUP155,
NUP205,POLA1,RRM1,SASS6,SMC2,WDHD1,XPO1
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 NUP107


There's no related Drug.
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Cross referenced IDs for NUP107
* 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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