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 ITPR2
Basic gene info.Gene symbolITPR2
Gene nameinositol 1,4,5-trisphosphate receptor, type 2
SynonymsCFAP48|IP3R2
CytomapUCSC genome browser: 12p11
Genomic locationchr12 :26488284-26986131
Type of geneprotein-coding
RefGenesNM_002223.2,
Ensembl idENSG00000123104
DescriptionIP3 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 date20141207
dbXrefs MIM : 600144
HGNC : HGNC
Ensembl : ENSG00000123104
HPRD : 02536
Vega : OTTHUMG00000169181
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ITPR2
BioGPS: 3709
Gene Expression Atlas: ENSG00000123104
The Human Protein Atlas: ENSG00000123104
PathwayNCI Pathway Interaction Database: ITPR2
KEGG: ITPR2
REACTOME: ITPR2
ConsensusPathDB
Pathway Commons: ITPR2
MetabolismMetaCyc: ITPR2
HUMANCyc: ITPR2
RegulationEnsembl's Regulation: ENSG00000123104
miRBase: chr12 :26,488,284-26,986,131
TargetScan: NM_002223
cisRED: ENSG00000123104
ContextiHOP: ITPR2
cancer metabolism search in PubMed: ITPR2
UCL Cancer Institute: ITPR2
Assigned class in ccmGDBC

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Phenotypic Information for ITPR2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ITPR2
MedGen: ITPR2 (Human Medical Genetics with Condition)
ClinVar: ITPR2
PhenotypeMGI: ITPR2 (International Mouse Phenotyping Consortium)
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.

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
liverITPR2chr122683506226835062ITPR2chr122696335126963351
ovaryITPR2chr122652563726525657RASSF8chr122619918326199203
ovaryITPR2chr122652790726527927ITPR2chr122652976426529784
ovaryITPR2chr122656571226565732ITPR2chr122653157126531591
ovaryITPR2chr122660767426607694TMTC1chr122966828329668303
ovaryITPR2chr122665718726657207ITPR2chr122666215026662170
ovaryITPR2chr122665719526657215ITPR2chr122666215026662170
ovaryITPR2chr122666955426669574chr122606535226065372
ovaryITPR2chr122667313726673157ITPR2chr122665270926652729
ovaryITPR2chr122672179426721814ITPR2chr122672202726722047
ovaryITPR2chr122677428226774302chr122833820828338228
ovaryITPR2chr122684345526843475ITPR2chr122685110626851126
ovaryITPR2chr122695795426957974ITPR2chr122696416626964186
ovaryITPR2chr122697819426978214ITPR2chr122697230626972326
ovaryITPR2chr122698486626984886chr122699103626991056
ovaryITPR2chr122698593626985956FGFR1OP2chr122710301227103032
pancreasITPR2chr122653473326534753chr123051310830513128
pancreasITPR2chr122653694526536965chr122805414528054165
pancreasITPR2chr122653837326538393ITPR2chr122660909226609112
pancreasITPR2chr122654175926541779chr122806379528063815
pancreasITPR2chr122660907026609090chr122632628826326308
pancreasITPR2chr122661801226618032chr123452637634526396
pancreasITPR2chr122662982126629841chr122806849228068512
pancreasITPR2chr122668176826681788chr123451089934510919
pancreasITPR2chr122672518226725202ITPR2chr122673209626732116
pancreasITPR2chr122672944426729464chr123059948130599501
pancreasITPR2chr122675112826751148ITPR2chr122676534626765366
pancreasITPR2chr122675308226753102chr125826442058264440
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 ITPR2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK122857ITPR2254965122683285326833562HOMER1961175857867174778742912
DA056326ITPR21232122664816126709255FAM59A233563182999286929993199
BF327272ZNF766177195277284652785401ITPR270331122664813226709260
AA526621ITPR2178122649018926490266ITPR262247122649025626490442
AI133642ITPR2183122685399926854081EIF58263014103800574103802408
AA525297ITPR2178122649018926490266ITPR262247122649025626490442
AL832587SUGP2514751191910373219141892ITPR247474772122653669526536720
BI027067POLDIP31210224298089342981107ITPR2209364122663332726633482
AW972739ITPR2116204122649018926490277ITPR2188373122649025626490442
BQ331543ARF322240124933378249334840ITPR2234508122695967626959951

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 # sample133 5  3 10 19  18 1
GAIN (# sample)133 5  2 10 19  18 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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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=6

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check002.gifSomatic 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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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
chr12:26839563-26839563p.R333R4
chr12:26640150-26640150p.K1802fs*133
chr12:26749897-26749897p.V1391V3
chr12:26714877-26714877p.R1547C3
chr12:26592234-26592234p.T2157A3
chr12:26818947-26818947p.V483I2
chr12:26811056-26811056p.D632Y2
chr12:26572040-26572040p.A2351V2
chr12:26818957-26818957p.L479L2
chr12:26572044-26572044p.V2350M2

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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
# sample8101385 101123 29147  1522425
# mutation9111465 111133 35147  1728441
nonsynonymous SNV771343 9 111 27117  1217430
synonymous SNV24 122 2122 83   511 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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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
chr12:26592234p.R1547C3
chr12:26839563p.T2157A3
chr12:26714877p.R333R3
chr12:26639109p.V483I2
chr12:26592232p.D1051N2
chr12:26572040p.I405V2
chr12:26868257p.S277I2
chr12:26818947p.A2351V2
chr12:26629871p.P358Q2
chr12:26868297p.R1934Q2

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 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

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

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
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 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



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