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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for IDI2 |
Basic gene info. | Gene symbol | IDI2 |
Gene name | isopentenyl-diphosphate delta isomerase 2 | |
Synonyms | IPPI2 | |
Cytomap | UCSC genome browser: 10p15.3 | |
Genomic location | chr10 :1064846-1071799 | |
Type of gene | protein-coding | |
RefGenes | NM_033261.2, | |
Ensembl id | ENSG00000148377 | |
Description | IPP isomerase 2diphosphate dimethylallyl diphosphate isomerase 2isopentenyl pyrophosphate isomerase 2isopentenyl-diphosphate Delta-isomerase 2isopentenyl-diphosphate delta-isomerase 2 | |
Modification date | 20141207 | |
dbXrefs | MIM : 615389 | |
HGNC : HGNC | ||
Ensembl : ENSG00000148377 | ||
HPRD : 17127 | ||
Vega : OTTHUMG00000017537 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_IDI2 | |
BioGPS: 91734 | ||
Gene Expression Atlas: ENSG00000148377 | ||
The Human Protein Atlas: ENSG00000148377 | ||
Pathway | NCI Pathway Interaction Database: IDI2 | |
KEGG: IDI2 | ||
REACTOME: IDI2 | ||
ConsensusPathDB | ||
Pathway Commons: IDI2 | ||
Metabolism | MetaCyc: IDI2 | |
HUMANCyc: IDI2 | ||
Regulation | Ensembl's Regulation: ENSG00000148377 | |
miRBase: chr10 :1,064,846-1,071,799 | ||
TargetScan: NM_033261 | ||
cisRED: ENSG00000148377 | ||
Context | iHOP: IDI2 | |
cancer metabolism search in PubMed: IDI2 | ||
UCL Cancer Institute: IDI2 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for IDI2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: IDI2 |
Familial Cancer Database: IDI2 |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: IDI2 |
MedGen: IDI2 (Human Medical Genetics with Condition) | |
ClinVar: IDI2 | |
Phenotype | MGI: IDI2 (International Mouse Phenotyping Consortium) |
PhenomicDB: IDI2 |
Mutations for IDI2 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows IDI2 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 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=16) | (# total SNVs=4) |
(# total SNVs=1) | (# total SNVs=0) |
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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 |
chr10:1068633-1068633 | p.V75V | 2 |
chr10:1066741-1066741 | p.R111H | 2 |
chr10:1065581-1065581 | p.A187G | 1 |
chr10:1066784-1066784 | p.E97K | 1 |
chr10:1070566-1070566 | p.A33V | 1 |
chr10:1065637-1065637 | p.T168T | 1 |
chr10:1066834-1066834 | p.Y80C | 1 |
chr10:1070568-1070568 | p.G32G | 1 |
chr10:1065705-1065705 | p.E146Q | 1 |
chr10:1066837-1066837 | p.G79A | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   | 1 | 4 | 1 |   |   |   | 2 |   |   | 1 | 2 | 1 |   |   | 3 | 2 |   | 2 |
# mutation | 3 |   | 1 | 4 | 1 |   |   |   | 2 |   |   | 1 | 2 | 1 |   |   | 3 | 2 |   | 2 |
nonsynonymous SNV | 3 |   |   | 2 | 1 |   |   |   | 2 |   |   |   | 2 | 1 |   |   | 1 | 1 |   | 1 |
synonymous SNV |   |   | 1 | 2 |   |   |   |   |   |   |   | 1 |   |   |   |   | 2 | 1 |   | 1 |
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 |
chr10:1066741 | p.R111H | 2 |
chr10:1066834 | p.V56I | 1 |
chr10:1065491 | p.X228X | 1 |
chr10:1066837 | p.E46E | 1 |
chr10:1065499 | p.P217P | 1 |
chr10:1068645 | p.E43K | 1 |
chr10:1065637 | p.P217Q | 1 |
chr10:1068692 | p.A33A | 1 |
chr10:1065705 | p.D214D | 1 |
chr10:1070526 | p.A33V | 1 |
Other DBs for Point Mutations |
Copy Number for IDI2 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 IDI2 |
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. |
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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 |
ATP5C1,SNHG15,CCT4,CDC123,DGUOK,FAM136A,GTPBP4, IDI2,KIN,LARP4B,LOC388796,MRTO4,NDUFAF4,NOP58, PDSS1,RANBP1,RBM17,RPIA,RPP38,RPS27A,SF3B14 | ANKRD23,ASB12,ASB5,CACNG1,CAPN3,DUSP26,FITM1, IDI2,JPH1,KCNA7,LRRC39,MB,MYADML2,MYBPH, MYH8,RYR1,SRPK3,TMEM38A,TNNI1,TNNI2,YIPF7 |
AGAP4,AGAP6,ANKRD16,LINC00852,C6orf163,CDK10,COMMD6, EBPL,IDI2,MSRB2,NANOS1,NSUN5P1,NSUN5P2,RPL11, RPS24,SPRN,TCTE3,TIAF1,UPF3A,ZNF692,ZNF789 | AKAP8,BCL3,BPY2,C6orf141,CHSY1,EGR4,EPHA2, FOSL1,FUT4,FUT5,IDI2,KIAA0040,KRT78,MESDC1, MMP13,OR2T12,OR52M1,PHLDA1,PNPLA5,SYCN,YTHDF1 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for IDI2 |
There's no related Drug. |
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Cross referenced IDs for IDI2 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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