Cancer Cell Metabolism Gene Database

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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 NPAS2
Basic gene info.Gene symbolNPAS2
Gene nameneuronal PAS domain protein 2
SynonymsMOP4|PASD4|bHLHe9
CytomapUCSC genome browser: 2q11.2
Genomic locationchr2 :101436612-101613287
Type of geneprotein-coding
RefGenesNM_002518.3,
Ensembl idENSG00000170485
DescriptionPAS domain-containing protein 4basic-helix-loop-helix-PAS protein MOP4class E basic helix-loop-helix protein 9member of PAS protein 4member of PAS superfamily 4neuronal PAS domain-containing protein 2neuronal PAS2
Modification date20141207
dbXrefs MIM : 603347
HGNC : HGNC
Ensembl : ENSG00000170485
HPRD : 09137
Vega : OTTHUMG00000130675
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NPAS2
BioGPS: 4862
Gene Expression Atlas: ENSG00000170485
The Human Protein Atlas: ENSG00000170485
PathwayNCI Pathway Interaction Database: NPAS2
KEGG: NPAS2
REACTOME: NPAS2
ConsensusPathDB
Pathway Commons: NPAS2
MetabolismMetaCyc: NPAS2
HUMANCyc: NPAS2
RegulationEnsembl's Regulation: ENSG00000170485
miRBase: chr2 :101,436,612-101,613,287
TargetScan: NM_002518
cisRED: ENSG00000170485
ContextiHOP: NPAS2
cancer metabolism search in PubMed: NPAS2
UCL Cancer Institute: NPAS2
Assigned class in ccmGDBC

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Phenotypic Information for NPAS2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NPAS2
Familial Cancer Database: NPAS2
* 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_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NPAS2
MedGen: NPAS2 (Human Medical Genetics with Condition)
ClinVar: NPAS2
PhenotypeMGI: NPAS2 (International Mouse Phenotyping Consortium)
PhenomicDB: NPAS2

Mutations for NPAS2
* 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
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryNPAS2chr2101448180101448200chr2101350594101350614
ovaryNPAS2chr2101480130101480150NPAS2chr2101480209101480229
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 NPAS2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW973590RPS6114091937632419376568NPAS21394622101541622101554305
CR991271NPAS255842101486976101487005KIAA0319L7781613594460435972739
AA553904RPS6621091937625919376568NPAS22094352101541622101549457
BQ365509NPAS2171642101486568101486715NPAS21583112101493443101493596

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     6 2    1   
GAIN (# sample)1       2        
LOSS (# sample)      6      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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=59)
Stat. for Synonymous SNVs
(# total SNVs=16)
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
chr2:101564740-101564740p.Q136R4
chr2:101549440-101549440p.E84*3
chr2:101598697-101598697p.S496L2
chr2:101604708-101604708p.L599L2
chr2:101609882-101609882p.V729F2
chr2:101591943-101591943p.E436K2
chr2:101580599-101580599p.F226F2
chr2:101554235-101554235p.I98I2
chr2:101584895-101584895p.?2
chr2:101594191-101594191p.S471L2

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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
# sample42112  2    755 210939
# mutation42112  2    854 21110311
nonsynonymous SNV1219  1    432 157 10
synonymous SNV3  3  1    422 16331
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
chr2:101564740p.Q136R4
chr2:101591324p.S400S3
chr2:101580599p.L599L2
chr2:101609882p.V729F2
chr2:101604708p.F226F2
chr2:101611915p.A410V1
chr2:101549457p.P586L1
chr2:101594255p.R824Q1
chr2:101580569p.F132F1
chr2:101584858p.L275Q1

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 NPAS2 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 NPAS2

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

APP,ATP1A1,CD58,CHRM3,COBL,DTNB,EPHA2,
EPHB1,ETV5,IFNGR2,IL22RA2,ITGA6,KCNN4,KDELR3,
MALL,MANSC1,NPAS2,SH3RF2,SLC45A3,SLC5A1,SOX10
C17orf100,CCDC120,CD3EAP,CELF5,CHMP4C,DTNB,ETV6,
GLS2,GRHL1,GYLTL1B,KCNC4,KCTD14,LPPR1,MANEAL,
NPAS2,PIK3C2G,SEMA4A,SH2D3A,SOX10,TFAP2C,TRAF3IP2

ASIC1,ATP11A,BCL2L1,BTBD16,FAM222B,TLDC2,CDK18,
CLCN2,CLDN1,CMTM7,ETV4,FGFR4,FOXQ1,IRF2BP2,
NCK2,NPAS2,RTKN,SH3TC2,SLCO4A1,TMC7,WFS1
CXorf23,ERBB3,FHDC1,HNF4A,KIAA1522,MTMR11,NPAS2,
NR3C2,OSBPL2,PDE8A,PHACTR2,RAB11FIP1,RAVER2,SLC8B1,
SLC26A6,TMEM164,TMEM170A,TMEM63B,TMUB2,VDR,WASL
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 NPAS2


There's no related Drug.
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Cross referenced IDs for NPAS2
* 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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