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 NPR2
Basic gene info.Gene symbolNPR2
Gene namenatriuretic peptide receptor 2
SynonymsAMDM|ANPRB|ANPb|ECDM|GUC2B|GUCY2B|NPRB|NPRBi
CytomapUCSC genome browser: 9p21-p12
Genomic locationchr9 :35792405-35809728
Type of geneprotein-coding
RefGenesNM_003995.3,
NM_000907.2,
Ensembl idENSG00000159899
DescriptionANP-BANPR-BGC-BNPR-Batrial natriuretic peptide B-type receptoratrial natriuretic peptide receptor 2atrial natriuretic peptide receptor type Bguanylate cyclase Bnatriuretic peptide receptor B/guanylate cyclase B (atrionatriuretic peptide receptor B
Modification date20141207
dbXrefs MIM : 108961
HGNC : HGNC
Ensembl : ENSG00000159899
HPRD : 00166
Vega : OTTHUMG00000019871
ProteinUniProt: P20594
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NPR2
BioGPS: 4882
Gene Expression Atlas: ENSG00000159899
The Human Protein Atlas: ENSG00000159899
PathwayNCI Pathway Interaction Database: NPR2
KEGG: NPR2
REACTOME: NPR2
ConsensusPathDB
Pathway Commons: NPR2
MetabolismMetaCyc: NPR2
HUMANCyc: NPR2
RegulationEnsembl's Regulation: ENSG00000159899
miRBase: chr9 :35,792,405-35,809,728
TargetScan: NM_003995
cisRED: ENSG00000159899
ContextiHOP: NPR2
cancer metabolism search in PubMed: NPR2
UCL Cancer Institute: NPR2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for NPR2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NPR2
Familial Cancer Database: NPR2
* 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
KEGG_PURINE_METABOLISM

check002.gifOthers
OMIM 108961; gene.
108961; gene.
602875; phenotype.
602875; phenotype.
Orphanet 329191; Tall stature - scoliosis - macrodactyly of the great toes.
329191; Tall stature - scoliosis - macrodactyly of the great toes.
40; Acromesomelic dysplasia, Maroteaux type.
40; Acromesomelic dysplasia, Maroteaux type.
DiseaseKEGG Disease: NPR2
MedGen: NPR2 (Human Medical Genetics with Condition)
ClinVar: NPR2
PhenotypeMGI: NPR2 (International Mouse Phenotyping Consortium)
PhenomicDB: NPR2

Mutations for NPR2
* 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 NPR2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ771511NPR21229793580943135809716ATHL129464211290940292602
L13436CASK4416X4144102941441441NPR2398408193579215235809729
BF369934NPR2179493579491335794991RASAL2916691178371899178372478

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 1        
GAIN (# sample)                 
LOSS (# sample)      1 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=9

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=78)
Stat. for Synonymous SNVs
(# total SNVs=20)
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
chr9:35805667-35805667p.K683Q9
chr9:35802269-35802269p.E567K3
chr9:35808513-35808513p.T907M3
chr9:35809413-35809413p.E1039Q3
chr9:35802771-35802771p.R620C3
chr9:35807326-35807326p.?3
chr9:35809214-35809214p.Q1016H2
chr9:35792534-35792534p.P43P2
chr9:35809392-35809392p.R1032*2
chr9:35802590-35802590p.R601C2

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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
# sample33 181 5 2  732 11415 14
# mutation53 201 5 2  1042 11816 16
nonsynonymous SNV32 14  5 1  342 11310 12
synonymous SNV21 61   1  7    56 4
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
chr9:35792877p.L889M2
chr9:35792411p.R745W2
chr9:35807348p.A2A2
chr9:35802240p.R557H2
chr9:35806091p.G158W2
chr9:35809214p.D444D1
chr9:35792578p.R601C1
chr9:35799675p.V868D1
chr9:35802274p.P61P1
chr9:35806228p.R1020Q1

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 NPR2 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 NPR2

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

BGN,BOC,CALD1,CHST3,CTGF,DDR2,GLI2,
LIX1L,LRP1,MSRB3,MYLK,NPR2,PRELP,PRICKLE1,
PROS1,PTRF,RECK,SNAI2,TIMP2,TMEM43,TSPAN18
ABCA8,ANKS6,DMGDH,EHD2,EPAS1,EPB41L2,FAM149A,
FAM26E,KANK2,LAMA4,LAMC1,MAP7D3,NPR2,NRP1,
PTPRM,SERPINF1,STXBP1,TBC1D2B,TK2,ZCCHC24,ZEB2

ARHGEF17,BNC2,TMEM240,C1R,DPYSL3,DZIP1,EFEMP2,
EMILIN1,EVC2,FAM110B,FBXL7,FGFR1,GYPC,HLX,
MAP3K12,MPDZ,MRAS,NPR2,PKD2,PNMAL2,ZNF667
ARHGEF17,BNC2,CD81,DIP2C,FGFR1,GLI3,GPRASP1,
LYNX1,NFATC4,NLGN2,NPR2,NRP2,PRELP,PTPRM,
RGAG4,RUSC2,SCN2B,TIMP2,TRPS1,ZBTB4,ZNF532
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 NPR2


There's no related Drug.
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Cross referenced IDs for NPR2
* 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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