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 ITPR2

Basic gene info.	Gene symbol	ITPR2
	Gene name	inositol 1,4,5-trisphosphate receptor, type 2
	Synonyms	CFAP48\|IP3R2
	Cytomap	UCSC genome browser: 12p11
	Genomic location	chr12 :26488284-26986131
	Type of gene	protein-coding
	RefGenes	NM_002223.2,
	Ensembl id	ENSG00000123104
	Description	IP3 receptorIP3R 2cilia and flagella associated protein 48inositol 1,4,5-triphosphate receptor, type 2inositol 1,4,5-trisphosphate receptor type 2insP3R2type 2 InsP3 receptortype 2 inositol 1,4,5-trisphosphate receptor
	Modification date	20141207
dbXrefs	MIM : 600144
	HGNC : HGNC
	Ensembl : ENSG00000123104
	HPRD : 02536
	Vega : OTTHUMG00000169181
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ITPR2
	BioGPS: 3709
	Gene Expression Atlas: ENSG00000123104
	The Human Protein Atlas: ENSG00000123104
Pathway	NCI Pathway Interaction Database: ITPR2
	KEGG: ITPR2
	REACTOME: ITPR2
	ConsensusPathDB
	Pathway Commons: ITPR2
Metabolism	MetaCyc: ITPR2
	HUMANCyc: ITPR2
Regulation	Ensembl's Regulation: ENSG00000123104
	miRBase: chr12 :26,488,284-26,986,131
	TargetScan: NM_002223
	cisRED: ENSG00000123104
Context	iHOP: ITPR2
	cancer metabolism search in PubMed: ITPR2
	UCL Cancer Institute: ITPR2
Assigned class in ccmGDB	C

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Phenotypic Information for ITPR2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ITPR2
	Familial Cancer Database: ITPR2

* 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
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: ITPR2
	MedGen: ITPR2 (Human Medical Genetics with Condition)
	ClinVar: ITPR2
Phenotype	MGI: ITPR2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ITPR2

Mutations for ITPR2

* 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

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
liver	ITPR2	chr12	26835062	26835062	ITPR2	chr12	26963351	26963351
ovary	ITPR2	chr12	26525637	26525657	RASSF8	chr12	26199183	26199203
ovary	ITPR2	chr12	26527907	26527927	ITPR2	chr12	26529764	26529784
ovary	ITPR2	chr12	26565712	26565732	ITPR2	chr12	26531571	26531591
ovary	ITPR2	chr12	26607674	26607694	TMTC1	chr12	29668283	29668303
ovary	ITPR2	chr12	26657187	26657207	ITPR2	chr12	26662150	26662170
ovary	ITPR2	chr12	26657195	26657215	ITPR2	chr12	26662150	26662170
ovary	ITPR2	chr12	26669554	26669574		chr12	26065352	26065372
ovary	ITPR2	chr12	26673137	26673157	ITPR2	chr12	26652709	26652729
ovary	ITPR2	chr12	26721794	26721814	ITPR2	chr12	26722027	26722047
ovary	ITPR2	chr12	26774282	26774302		chr12	28338208	28338228
ovary	ITPR2	chr12	26843455	26843475	ITPR2	chr12	26851106	26851126
ovary	ITPR2	chr12	26957954	26957974	ITPR2	chr12	26964166	26964186
ovary	ITPR2	chr12	26978194	26978214	ITPR2	chr12	26972306	26972326
ovary	ITPR2	chr12	26984866	26984886		chr12	26991036	26991056
ovary	ITPR2	chr12	26985936	26985956	FGFR1OP2	chr12	27103012	27103032
pancreas	ITPR2	chr12	26534733	26534753		chr12	30513108	30513128
pancreas	ITPR2	chr12	26536945	26536965		chr12	28054145	28054165
pancreas	ITPR2	chr12	26538373	26538393	ITPR2	chr12	26609092	26609112
pancreas	ITPR2	chr12	26541759	26541779		chr12	28063795	28063815
pancreas	ITPR2	chr12	26609070	26609090		chr12	26326288	26326308
pancreas	ITPR2	chr12	26618012	26618032		chr12	34526376	34526396
pancreas	ITPR2	chr12	26629821	26629841		chr12	28068492	28068512
pancreas	ITPR2	chr12	26681768	26681788		chr12	34510899	34510919
pancreas	ITPR2	chr12	26725182	26725202	ITPR2	chr12	26732096	26732116
pancreas	ITPR2	chr12	26729444	26729464		chr12	30599481	30599501
pancreas	ITPR2	chr12	26751128	26751148	ITPR2	chr12	26765346	26765366
pancreas	ITPR2	chr12	26753082	26753102		chr12	58264420	58264440

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 ITPR2 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
AK122857	ITPR2	254	965	12	26832853	26833562	HOMER1	961	1758	5	78671747	78742912
DA056326	ITPR2	1	232	12	26648161	26709255	FAM59A	233	563	18	29992869	29993199
BF327272	ZNF766	1	77	19	52772846	52785401	ITPR2	70	331	12	26648132	26709260
AA526621	ITPR2	1	78	12	26490189	26490266	ITPR2	62	247	12	26490256	26490442
AI133642	ITPR2	1	83	12	26853999	26854081	EIF5	82	630	14	103800574	103802408
AA525297	ITPR2	1	78	12	26490189	26490266	ITPR2	62	247	12	26490256	26490442
AL832587	SUGP2	51	4751	19	19103732	19141892	ITPR2	4747	4772	12	26536695	26536720
BI027067	POLDIP3	1	210	22	42980893	42981107	ITPR2	209	364	12	26633327	26633482
AW972739	ITPR2	116	204	12	26490189	26490277	ITPR2	188	373	12	26490256	26490442
BQ331543	ARF3	22	240	12	49333782	49334840	ITPR2	234	508	12	26959676	26959951

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	13	3		5			3		10		19			1	8		1
GAIN (# sample)	13	3		5			2		10		19			1	8		1
LOSS (# sample)							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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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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=231)	Stat. for Synonymous SNVs (# total SNVs=61)

Stat. for Deletions (# total SNVs=7)	Stat. for Insertions (# total SNVs=1)

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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
chr12:26839563-26839563	p.R333R	4
chr12:26640150-26640150	p.K1802fs*13	3
chr12:26749897-26749897	p.V1391V	3
chr12:26714877-26714877	p.R1547C	3
chr12:26592234-26592234	p.T2157A	3
chr12:26818947-26818947	p.V483I	2
chr12:26811056-26811056	p.D632Y	2
chr12:26572040-26572040	p.A2351V	2
chr12:26818957-26818957	p.L479L	2
chr12:26572044-26572044	p.V2350M	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=5

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	8	10	1	38	5		10	1	12	3		29	14	7			15	22	4	25
# mutation	9	11	1	46	5		11	1	13	3		35	14	7			17	28	4	41
nonsynonymous SNV	7	7	1	34	3		9		11	1		27	11	7			12	17	4	30
synonymous SNV	2	4		12	2		2	1	2	2		8	3				5	11		11

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
chr12:26592234	p.R1547C	3
chr12:26839563	p.T2157A	3
chr12:26714877	p.R333R	3
chr12:26639109	p.V483I	2
chr12:26592232	p.D1051N	2
chr12:26572040	p.I405V	2
chr12:26868257	p.S277I	2
chr12:26818947	p.A2351V	2
chr12:26629871	p.P358Q	2
chr12:26868297	p.R1934Q	2

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 ITPR2 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 ITPR2

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


AFP,FAM169A,FBXL7,GPATCH2,ITPR2,KIAA1109,KIF3A, KLHDC10,KRBA2,MED13L,NAPB,NCOR1,PCDH19,PHF3, RASSF6,RUFY2,SEZ6L,TBC1D12,WBP11,ZFYVE9,ZKSCAN8	ANKRD17,B3GALT5,CSRNP3,DHX33,DSC2,EHF,GPR98, GTF3C4,HCG18,ITPR2,MBTD1,MCM3AP-AS1,MGA,MLLT4, N4BP2,NFXL1,SETD5,TET2,TET3,WRN,ZNF562

ARID2,BEST3,CADM1,EPC2,FGF20,ITPR2,LEF1, LRP6,MAN1A1,MED13L,NFE2,NOTCH1,NRXN3,PMFBP1, PROX1,RASL11B,SLC4A8,SOX6,TP53BP1,UTRN,ZBTB39	ADCY1,ANKRD17,ANKRD26,ARAP3,ASXL2,FAM208A,DPY19L3, GIGYF2,ITPR2,KIAA1244,MFHAS1,MGA,MKL2,PHF8, PROX1,RBM12B,SMARCC1,TAF1,TPR,USP24,ZKSCAN1

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 ITPR2

There's no related Drug.

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Cross referenced IDs for ITPR2

* 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