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 NUPL2
Basic gene info.Gene symbolNUPL2
Gene namenucleoporin like 2
SynonymsCG1|NLP-1|NLP_1|hCG1
CytomapUCSC genome browser: 7p15
Genomic locationchr7 :23221445-23240630
Type of geneprotein-coding
RefGenesNM_007342.2,
Ensembl idENSG00000136243
DescriptionH_RG271G13.9NUP42 homolognucleoporin hCG1nucleoporin-like protein 1nucleoporin-like protein 2
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000136243
HPRD : 14855
Vega : OTTHUMG00000096955
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NUPL2
BioGPS: 11097
Gene Expression Atlas: ENSG00000136243
The Human Protein Atlas: ENSG00000136243
PathwayNCI Pathway Interaction Database: NUPL2
KEGG: NUPL2
REACTOME: NUPL2
ConsensusPathDB
Pathway Commons: NUPL2
MetabolismMetaCyc: NUPL2
HUMANCyc: NUPL2
RegulationEnsembl's Regulation: ENSG00000136243
miRBase: chr7 :23,221,445-23,240,630
TargetScan: NM_007342
cisRED: ENSG00000136243
ContextiHOP: NUPL2
cancer metabolism search in PubMed: NUPL2
UCL Cancer Institute: NUPL2
Assigned class in ccmGDBC

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Phenotypic Information for NUPL2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NUPL2
Familial Cancer Database: NUPL2
* 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: NUPL2
MedGen: NUPL2 (Human Medical Genetics with Condition)
ClinVar: NUPL2
PhenotypeMGI: NUPL2 (International Mouse Phenotyping Consortium)
PhenomicDB: NUPL2

Mutations for NUPL2
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NUPL2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CR984678NUPL2148472322166623226765TMC8483772177613749676137787

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 # sample          1      
GAIN (# sample)          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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=36)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=7)

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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
chr7:23221797-23221798p.G31_R32insRQQP5
chr7:23236306-23236306p.S177F3
chr7:23235512-23235512p.T167N2
chr7:23224773-23224773p.G71fs*512
chr7:23240069-23240069p.G326V2
chr7:23240239-23240239p.D383Y2
chr7:23240124-23240124p.G344G2
chr7:23240128-23240128p.G346C2
chr7:23239114-23239114p.P216L2
chr7:23239115-23239115p.P216P2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample31 81 1 3  321  46 7
# mutation31 81 1 3  321  36 8
nonsynonymous SNV31 71   3  321  23 7
synonymous SNV   1  1         13 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])

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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
chr7:23236306p.S177F3
chr7:23239115p.P216P2
chr7:23240207p.S372Y2
chr7:23240239p.D383H2
chr7:23240041p.G24R1
chr7:23226676p.P216L1
chr7:23239157p.N366K1
chr7:23240047p.N43S1
chr7:23226687p.S370T1
chr7:23239787p.R45R1

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 NUPL2 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 NUPL2

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

CCDC172,MALSU1,FAM221A,CBX3,CDCA7L,CYCS,DKFZP586I1420,
SPATA31D4,SPATA31D3,GARS,HIBADH,KLHL7,LOC285954,LSM5,
NOD1,NUPL2,RP9,RP9P,SH2D4B,TOMM7,TRA2A
VCPKMT,C5orf28,TDRP,CBFB,COIL,COMMD2,DIMT1,
E2F5,FAM60A,MED17,MTHFD2L,NUFIP1,NUPL2,PACRGL,
PI4K2B,PRKCI,PUS7,RNF138,TMEM123,TMPO,TWISTNB

AIMP2,BZW2,MPLKIP,C7orf25,MALSU1,COA1,CBX3,
CCT6A,CYCS,DDX56,EIF2AK1,GGCT,HIBADH,LSM5,
MIOS,MRPL32,MRPS17,NUPL2,PSMA2,TBRG4,TWISTNB
ANKRD49,C12orf29,C12orf73,DTD2,C5orf28,TRAPPC13,TRMT13,
COMMD10,INTS10,LYRM2,MRPL32,MTHFD2L,NUPL2,PCID2,
PDCD2,RPAIN,RPS3A,RPS7,TMEM14B,TMEM223,TRUB1
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 NUPL2


There's no related Drug.
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Cross referenced IDs for NUPL2
* 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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