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 symbolITPR3
Gene nameinositol 1,4,5-trisphosphate receptor, type 3
SynonymsIP3R|IP3R3
CytomapUCSC genome browser: 6p21
Genomic locationchr6 :33589155-33664348
Type of geneprotein-coding
RefGenesNM_002224.3,
Ensembl idENSG00000096433
DescriptionIP3 receptorinositol 1,4,5-triphosphate receptor, type 3inositol 1,4,5-trisphosphate receptor type 3insP3R3type 3 InsP3 receptor
Modification date20141207
dbXrefs MIM : 147267
HGNC : HGNC
Ensembl : ENSG00000096433
HPRD : 00926
Vega : OTTHUMG00000014532
ProteinUniProt: Q14573
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ITPR3
BioGPS: 3710
Gene Expression Atlas: ENSG00000096433
The Human Protein Atlas: ENSG00000096433
PathwayNCI Pathway Interaction Database: ITPR3
KEGG: ITPR3
REACTOME: ITPR3
ConsensusPathDB
Pathway Commons: ITPR3
MetabolismMetaCyc: ITPR3
HUMANCyc: ITPR3
RegulationEnsembl's Regulation: ENSG00000096433
miRBase: chr6 :33,589,155-33,664,348
TargetScan: NM_002224
cisRED: ENSG00000096433
ContextiHOP: ITPR3
cancer metabolism search in PubMed: ITPR3
UCL Cancer Institute: ITPR3
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ITPR3 in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM 147267; gene.
Orphanet
DiseaseKEGG Disease: ITPR3
MedGen: ITPR3 (Human Medical Genetics with Condition)
ClinVar: ITPR3
PhenotypeMGI: ITPR3 (International Mouse Phenotyping Consortium)
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.

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
* 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastITPR3chr63360683433606834PTCHD4chr64794554747945547
ovaryITPR3chr63363573633635756ITPR3chr63363578633635806
pancreasITPR3chr63364233233642352chr163526461035264630
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 ITPR3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA507809ITPR3510463366280533663532ITPR310027863366141433662810
CB306680ITPR3186963366205633662107ITPR36525963366225133662444
BF848867ITPR31722963365805133658263FXR22303281774992897504801
BF762968AARS1241167028767270289887ITPR323438963363563133636336
BF763529ITPR3113163364817833648408SETD5125357395168559517087
BF954113ITPR31722963365805133658263FXR22303281774992897504801

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         2      
GAIN (# sample)1         2      
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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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=5

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check002.gifSomatic 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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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
chr6:33660616-33660616p.R2524C4
chr6:33635629-33635629p.E592K3
chr6:33648197-33648197p.T1439M3
chr6:33634933-33634933p.R527C3
chr6:33634906-33634906p.V518I3
chr6:33638469-33638469p.A821A3
chr6:33625713-33625713p.A96V3
chr6:33653882-33653882p.T1907M3
chr6:33653448-33653448p.G1837G2
chr6:33608316-33608316p.P49S2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample77 448 8 61217751 1535 23
# mutation87 5010 8 61218851 1746 28
nonsynonymous SNV55 378 3 4111544  633 18
synonymous SNV32 132 5 2 13411 1113 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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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
chr6:33638469p.A821A3
chr6:33625713p.E702E2
chr6:33657928p.R2271H2
chr6:33655304p.P525P2
chr6:33635679p.T1907M2
chr6:33641396p.R2076H2
chr6:33660616p.H2638R2
chr6:33657132p.D2317N2
chr6:33636358p.R2524C2
chr6:33623571p.N63N2

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 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

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

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
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 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



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