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 ITPR3

Basic gene info.	Gene symbol	ITPR3
	Gene name	inositol 1,4,5-trisphosphate receptor, type 3
	Synonyms	IP3R\|IP3R3
	Cytomap	UCSC genome browser: 6p21
	Genomic location	chr6 :33589155-33664348
	Type of gene	protein-coding
	RefGenes	NM_002224.3,
	Ensembl id	ENSG00000096433
	Description	IP3 receptorinositol 1,4,5-triphosphate receptor, type 3inositol 1,4,5-trisphosphate receptor type 3insP3R3type 3 InsP3 receptor
	Modification date	20141207
dbXrefs	MIM : 147267
	HGNC : HGNC
	Ensembl : ENSG00000096433
	HPRD : 00926
	Vega : OTTHUMG00000014532
Protein	UniProt: Q14573 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ITPR3
	BioGPS: 3710
	Gene Expression Atlas: ENSG00000096433
	The Human Protein Atlas: ENSG00000096433
Pathway	NCI Pathway Interaction Database: ITPR3
	KEGG: ITPR3
	REACTOME: ITPR3
	ConsensusPathDB
	Pathway Commons: ITPR3
Metabolism	MetaCyc: ITPR3
	HUMANCyc: ITPR3
Regulation	Ensembl's Regulation: ENSG00000096433
	miRBase: chr6 :33,589,155-33,664,348
	TargetScan: NM_002224
	cisRED: ENSG00000096433
Context	iHOP: ITPR3
	cancer metabolism search in PubMed: ITPR3
	UCL Cancer Institute: ITPR3
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ITPR3 in cancer cell metabolism	1. Sumantran VN, Mishra P, Sudhakar N (2015) Microarray analysis of differentially expressed genes regulating lipid metabolism during melanoma progression. Indian J Biochem Biophys 52: 125-131. go to article

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Phenotypic Information for ITPR3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ITPR3
	Familial Cancer Database: ITPR3

* 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	147267; gene.
Orphanet
Disease	KEGG Disease: ITPR3
	MedGen: ITPR3 (Human Medical Genetics with Condition)
	ClinVar: ITPR3
Phenotype	MGI: ITPR3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ITPR3

Mutations for ITPR3

* 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
breast	ITPR3	chr6	33606834	33606834	PTCHD4	chr6	47945547	47945547
ovary	ITPR3	chr6	33635736	33635756	ITPR3	chr6	33635786	33635806
pancreas	ITPR3	chr6	33642332	33642352		chr16	35264610	35264630

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 ITPR3 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
AA507809	ITPR3	5	104	6	33662805	33663532	ITPR3	100	278	6	33661414	33662810
CB306680	ITPR3	18	69	6	33662056	33662107	ITPR3	65	259	6	33662251	33662444
BF848867	ITPR3	17	229	6	33658051	33658263	FXR2	230	328	17	7499289	7504801
BF762968	AARS	1	241	16	70287672	70289887	ITPR3	234	389	6	33635631	33636336
BF763529	ITPR3	1	131	6	33648178	33648408	SETD5	125	357	3	9516855	9517087
BF954113	ITPR3	17	229	6	33658051	33658263	FXR2	230	328	17	7499289	7504801

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=199)	Stat. for Synonymous SNVs (# total SNVs=62)

Stat. for Deletions (# total SNVs=8)	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
chr6:33660616-33660616	p.R2524C	4
chr6:33634906-33634906	p.V518I	3
chr6:33638469-33638469	p.A821A	3
chr6:33625713-33625713	p.A96V	3
chr6:33653882-33653882	p.T1907M	3
chr6:33635629-33635629	p.E592K	3
chr6:33648197-33648197	p.T1439M	3
chr6:33634933-33634933	p.R527C	3
chr6:33653213-33653213	p.R1795R	2
chr6:33655066-33655066	p.R2047C	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	7	7		44	8		8		6	1	2	17	7	5	1		15	35		23
# mutation	8	7		50	10		8		6	1	2	18	8	5	1		17	46		28
nonsynonymous SNV	5	5		37	8		3		4	1	1	15	4	4			6	33		18
synonymous SNV	3	2		13	2		5		2		1	3	4	1	1		11	13		10

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
chr6:33638469	p.A821A	3
chr6:33657132	p.N63N	2
chr6:33636358	p.T2329A	2
chr6:33623571	p.A821T	2
chr6:33638467	p.R986H	2
chr6:33653882	p.K608K	2
chr6:33634929	p.A96V	2
chr6:33662828	p.L651L	2
chr6:33657892	p.E702E	2
chr6:33636850	p.R2271H	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 ITPR3 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 ITPR3

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


ARHGAP11B,PRRC2A,CENPO,CKAP2L,CLSPN,DNMT1,FOXM1, HCFC1,INCENP,ITPR3,KIFC1,MCM3,MCM6,MKI67, MSH2,MSH6,NCAPD2,SMC2,TCF19,TOPBP1,ZNF367	CCDC57,DNMT1,ESRP2,ITPR3,KDM5C,KIAA0556,KIAA1244, MST1R,MYO19,NBEAL2,PIGO,RAI1,SEC16A,SEC24C, SLC26A1,SPATA13,SPTBN2,SRCAP,TRIM36,ZNF710,ZSWIM5

ANKRD11,ANKS1A,PRR14L,CASZ1,DOT1L,GNA11,GOLGA4, IQGAP3,ITPR3,CEP170B,MYO18A,PCNT,PLEKHA7,RREB1, SPEN,SRRM2,TMEM63B,UBR2,UBR4,ZNF318,ZZEF1	AP1B1,ARHGAP32,PRR14L,CLEC16A,CNOT1,DSP,EXT1, GAK,ITGB4,ITPR3,AREL1,MYH14,MYO18A,PCNXL3, PDPK1,PLXNA2,RAB11FIP4,RRBP1,RREB1,TRAPPC10,ZZEF1

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 ITPR3

There's no related Drug.

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Cross referenced IDs for ITPR3

* 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