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 NCBP2
Basic gene info.Gene symbolNCBP2
Gene namenuclear cap binding protein subunit 2, 20kDa
SynonymsCBC2|CBP20|NIP1
CytomapUCSC genome browser: 3q29
Genomic locationchr3 :196662272-196669464
Type of geneprotein-coding
RefGenesNM_001042540.1,
NM_007362.3,
Ensembl idENSG00000114503
Description20 kDa nuclear cap-binding proteinNCBP 20 kDa subunitNCBP interacting protein 1NCBP-interacting protein 1cell proliferation-inducing gene 55 proteinnuclear cap binding protein subunit 2, 20kDnuclear cap-binding protein subunit 2
Modification date20141207
dbXrefs MIM : 605133
HGNC : HGNC
Ensembl : ENSG00000114503
HPRD : 05503
Vega : OTTHUMG00000155520
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NCBP2
BioGPS: 22916
Gene Expression Atlas: ENSG00000114503
The Human Protein Atlas: ENSG00000114503
PathwayNCI Pathway Interaction Database: NCBP2
KEGG: NCBP2
REACTOME: NCBP2
ConsensusPathDB
Pathway Commons: NCBP2
MetabolismMetaCyc: NCBP2
HUMANCyc: NCBP2
RegulationEnsembl's Regulation: ENSG00000114503
miRBase: chr3 :196,662,272-196,669,464
TargetScan: NM_001042540
cisRED: ENSG00000114503
ContextiHOP: NCBP2
cancer metabolism search in PubMed: NCBP2
UCL Cancer Institute: NCBP2
Assigned class in ccmGDBC

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Phenotypic Information for NCBP2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NCBP2
Familial Cancer Database: NCBP2
* 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_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NCBP2
MedGen: NCBP2 (Human Medical Genetics with Condition)
ClinVar: NCBP2
PhenotypeMGI: NCBP2 (International Mouse Phenotyping Consortium)
PhenomicDB: NCBP2

Mutations for NCBP2
* 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
pancreasNCBP2chr3196662594196662614MAST4chr56641401766414037
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 NCBP2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA659977NCBP21813196669297196669377FBXL28256933340076933415357
AA625748NCBP2543923196662329196662667PEX53935481273622797362434
BU536214YBX1426614314809843148360NCBP22674973196663726196663955
F01144NCBP211773196662339196662515GDF91753375132202339132202681

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)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=14)
Stat. for Synonymous SNVs
(# total SNVs=3)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr3:196664391-196664391p.S130Y2
chr3:196664509-196664509p.R91C1
chr3:196666226-196666226p.T52T1
chr3:196664404-196664404p.G126S1
chr3:196666252-196666252p.V44F1
chr3:196664405-196664405p.Y125Y1
chr3:196666260-196666260p.T41M1
chr3:196664431-196664431p.A117T1
chr3:196669315-196669315p.Y20*1
chr3:196664432-196664432p.D116D1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   51 2    1     1 4
# mutation   41 2    1     1 4
nonsynonymous SNV   21 2    1       3
synonymous SNV   2             1 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
chr3:196664498p.A41A,NCBP22
chr3:196664405p.I57M,NCBP21
chr3:196664432p.R56Q,NCBP21
chr3:196664450p.R46Q,NCBP21
chr3:196664454p.R46W,NCBP21
chr3:196664484p.T52T1
chr3:196664485p.L6Q,NCBP21
chr3:196663898p.S2T,NCBP21
chr3:196666226p.L99P,NCBP21
chr3:196663927p.Y89Y,NCBP21

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 NCBP2 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 NCBP2

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

ACTL6A,DLG1,DNAJB11,DVL3,FBXO45,FXR1,FYTTD1,
LOC220729,LSG1,MRPL47,NCBP2,OPA1,PAK2,PARL,
PIGX,RFC4,SENP5,TBCCD1,TMEM41A,TRA2B,WDR53
SMIM15,CAND1,CCT2,CNOT2,COPB1,DCAF13,HNRNPK,
ITFG1,NCBP2,NUP107,PIGX,RAB22A,RARS,SLMO2,
SMARCE1,SUB1,THUMPD3,TWF1,UBE2K,VPS35,YEATS4

ACVR2B,ALG3,ANAPC13,ATP13A3,CMTM8,DDX27,DNAJC19,
E2F3,FBXO45,IGF2BP2,LOC152217,MPHOSPH10,NCBP2,RAB7A,
RNF114,SENP5,U2SURP,TMEM41A,TSEN2,UBE2V1,WDR53
URI1,DNAI2,TVP23B,GAB1,GABPA,HDHD2,NCBP2,
P4HA1,PPP3CA,DESI2,PSG9,SMAD1,SPHAR,SPOPL,
SYTL4,TLK1,TMC1,TMEM30A,WEE2,ZNF24,ZNF442
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 NCBP2


There's no related Drug.
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Cross referenced IDs for NCBP2
* 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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