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 IDI1
Basic gene info.Gene symbolIDI1
Gene nameisopentenyl-diphosphate delta isomerase 1
SynonymsIPP1|IPPI1
CytomapUCSC genome browser: 10p15.3
Genomic locationchr10 :1085963-1095061
Type of geneprotein-coding
RefGenesNM_004508.2,
Ensembl idENSG00000067064
DescriptionIPP isomerase 1isopentenyl diphosphate dimethylallyl diphosphate isomerase 1isopentenyl pyrophosphate isomerase 1isopentenyl-diphosphate Delta-isomerase 1
Modification date20141207
dbXrefs MIM : 604055
HGNC : HGNC
Ensembl : ENSG00000067064
HPRD : 07235
Vega : OTTHUMG00000017536
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_IDI1
BioGPS: 3422
Gene Expression Atlas: ENSG00000067064
The Human Protein Atlas: ENSG00000067064
PathwayNCI Pathway Interaction Database: IDI1
KEGG: IDI1
REACTOME: IDI1
ConsensusPathDB
Pathway Commons: IDI1
MetabolismMetaCyc: IDI1
HUMANCyc: IDI1
RegulationEnsembl's Regulation: ENSG00000067064
miRBase: chr10 :1,085,963-1,095,061
TargetScan: NM_004508
cisRED: ENSG00000067064
ContextiHOP: IDI1
cancer metabolism search in PubMed: IDI1
UCL Cancer Institute: IDI1
Assigned class in ccmGDBC

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Phenotypic Information for IDI1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: IDI1
Familial Cancer Database: IDI1
* 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_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: IDI1
MedGen: IDI1 (Human Medical Genetics with Condition)
ClinVar: IDI1
PhenotypeMGI: IDI1 (International Mouse Phenotyping Consortium)
PhenomicDB: IDI1

Mutations for IDI1
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows IDI1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE708329IDI111781010913381091515CRTC3170246159112212991122205

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
There's no copy number variation information in COSMIC data for this gene.

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=25)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=1)
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
chr10:1094906-1094906p.C13Y3
chr10:1087227-1087227p.P252L2
chr10:1088646-1088646p.E155K2
chr10:1094902-1094902p.A14A2
chr10:1088574-1088574p.E179Q1
chr10:1089330-1089330p.L106*1
chr10:1088607-1088607p.R168G1
chr10:1089975-1089975p.K93*1
chr10:1094909-1094909p.G12A1
chr10:1087243-1087243p.E247K1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 2  1     1   1  2
# mutation 2 2  1     1   2  3
nonsynonymous SNV 2 1  1     1   1  3
synonymous SNV   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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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
chr10:1087317p.P222H1
chr10:1087328p.L218F1
chr10:1088638p.D157D1
chr10:1088646p.E155K1
chr10:1089276p.L124R1
chr10:1089294p.T118I1
chr10:1089327p.L107S1
chr10:1089329p.L106F1
chr10:1090086p.V56L1
chr10:1087205p.L49I1

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 IDI1 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 IDI1

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

AACS,AKR1B15,AKR1D1,C6orf223,FCN2,GSTM5,GUSB,
IDI1,ISX,LOC91948,LST-3TM12,MYOM2,PNLIPRP3,RLN3,
RNASE11,RNASE12,MSMO1,SLCO1B1,SPINK8,SRD5A1,SULT1C3
ABCC12,ACSL3,ADAM2,ALOX15B,APOD,C15orf43,DHRS2,
EPS8L3,HIST1H2AG,HPGD,IDI1,IYD,LST-3TM12,MPV17L,
RNASE12,SERHL2,SERHL,SULT1C3,TMPRSS11F,UGT2B10,UGT2B11

ACAT2,ATP5C1,CYP51A1,DBI,DHCR24,DHCR7,EBP,
FDPS,GHITM,HMGCR,HMGCS1,HSD17B7,HSPA14,IDH1,
IDI1,INSIG1,MVD,PDCD10,MSMO1,SC5D,STARD4
ACAT2,C14orf1,DNAJA1,EBP,ELOVL6,FDFT1,FDPS,
HMGCS1,HSD17B7,IDI1,INSIG1,MVK,NSDHL,PLA2G3,
PPA1,PRND,PSMA3,RDH11,MSMO1,SC5D,STARD4
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 IDI1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01785isopentenyl-diphosphate delta isomerase 1experimentalDimethylallyl Diphosphate


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Cross referenced IDs for IDI1
* 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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