Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 NPR2

Basic gene info.	Gene symbol	NPR2
	Gene name	natriuretic peptide receptor 2
	Synonyms	AMDM\|ANPRB\|ANPb\|ECDM\|GUC2B\|GUCY2B\|NPRB\|NPRBi
	Cytomap	UCSC genome browser: 9p21-p12
	Genomic location	chr9 :35792405-35809728
	Type of gene	protein-coding
	RefGenes	NM_003995.3, NM_000907.2,
	Ensembl id	ENSG00000159899
	Description	ANP-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 date	20141207
dbXrefs	MIM : 108961
	HGNC : HGNC
	Ensembl : ENSG00000159899
	HPRD : 00166
	Vega : OTTHUMG00000019871
Protein	UniProt: P20594 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NPR2
	BioGPS: 4882
	Gene Expression Atlas: ENSG00000159899
	The Human Protein Atlas: ENSG00000159899
Pathway	NCI Pathway Interaction Database: NPR2
	KEGG: NPR2
	REACTOME: NPR2
	ConsensusPathDB
	Pathway Commons: NPR2
Metabolism	MetaCyc: NPR2
	HUMANCyc: NPR2
Regulation	Ensembl's Regulation: ENSG00000159899
	miRBase: chr9 :35,792,405-35,809,728
	TargetScan: NM_003995
	cisRED: ENSG00000159899
Context	iHOP: NPR2
	cancer metabolism search in PubMed: NPR2
	UCL Cancer Institute: NPR2
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for NPR2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_PURINE_METABOLISM

Others
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.
Disease	KEGG Disease: NPR2
	MedGen: NPR2 (Human Medical Genetics with Condition)
	ClinVar: NPR2
Phenotype	MGI: NPR2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NPR2 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BQ771511	NPR2	12	297	9	35809431	35809716	ATHL1	294	642	11	290940	292602
L13436	CASK	4	416	X	41441029	41441441	NPR2	398	4081	9	35792152	35809729
BF369934	NPR2	17	94	9	35794913	35794991	RASAL2	91	669	1	178371899	178372478

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr9:35805667-35805667	p.K683Q	9
chr9:35802269-35802269	p.E567K	3
chr9:35808513-35808513	p.T907M	3
chr9:35809413-35809413	p.E1039Q	3
chr9:35802771-35802771	p.R620C	3
chr9:35807326-35807326	p.?	3
chr9:35792534-35792534	p.P43P	2
chr9:35809392-35809392	p.R1032*	2
chr9:35802590-35802590	p.R601C	2
chr9:35800819-35800819	p.D444D	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	3	3		18	1		5		2			7	3	2		1	14	15		14
# mutation	5	3		20	1		5		2			10	4	2		1	18	16		16
nonsynonymous SNV	3	2		14			5		1			3	4	2		1	13	10		12
synonymous SNV	2	1		6	1				1			7					5	6		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr9:35792877	p.R745W	2
chr9:35792411	p.A2A	2
chr9:35807348	p.R557H	2
chr9:35802240	p.G158W	2
chr9:35806091	p.L889M	2
chr9:35793935	p.R218Q	1
chr9:35801716	p.Q353P	1
chr9:35808587	p.E486K	1
chr9:35799693	p.R620H	1
chr9:35802590	p.I896T	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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