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 IDUA
Basic gene info.Gene symbolIDUA
Gene nameiduronidase, alpha-L-
SynonymsIDA|MPS1
CytomapUCSC genome browser: 4p16.3
Genomic locationchr4 :980784-998317
Type of geneprotein-coding
RefGenesNM_000203.4,
NR_110313.1,
Ensembl idENSG00000127415
Descriptionalpha-L-iduronidase
Modification date20141219
dbXrefs MIM : 252800
HGNC : HGNC
Ensembl : ENSG00000127415
HPRD : 02016
Vega : OTTHUMG00000088901
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_IDUA
BioGPS: 3425
Gene Expression Atlas: ENSG00000127415
The Human Protein Atlas: ENSG00000127415
PathwayNCI Pathway Interaction Database: IDUA
KEGG: IDUA
REACTOME: IDUA
ConsensusPathDB
Pathway Commons: IDUA
MetabolismMetaCyc: IDUA
HUMANCyc: IDUA
RegulationEnsembl's Regulation: ENSG00000127415
miRBase: chr4 :980,784-998,317
TargetScan: NM_000203
cisRED: ENSG00000127415
ContextiHOP: IDUA
cancer metabolism search in PubMed: IDUA
UCL Cancer Institute: IDUA
Assigned class in ccmGDBC

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

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

Mutations for IDUA
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryIDUAchr4996268996288WDFY3-AS2chr48592265085922670
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 IDUA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW136332IDUA13274996572997176IDUA3233824997823997882
BE939137FAM134C179174073251240732590IDUA762254992259992408

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=21)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr4:996165-996165p.A361T2
chr4:995923-995923p.V316M2
chr4:996888-996888p.R489R2
chr4:995272-995272p.A170A2
chr4:995294-995294p.E178K2
chr4:996138-996138p.F352L1
chr4:980873-980873p.M1V1
chr4:995327-995327p.D189H1
chr4:998057-998057p.A613V1
chr4:995790-995790p.S271S1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 22 3 1  11   55 6
# mutation 1 22 3 1  12   56 6
nonsynonymous SNV 1 2  3 1   2   32 5
synonymous SNV    2      1    24 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
chr4:995272p.A170A2
chr4:995294p.E178K2
chr4:980873p.Q281P1
chr4:995592p.M1V1
chr4:997818p.Y343Y1
chr4:994704p.F140L1
chr4:995599p.Y167H1
chr4:998057p.N348N1
chr4:995261p.N350N1
chr4:995665p.W175R1

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 IDUA 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 IDUA

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

ANKS3,LMNTD2,CCDC24,D2HGDH,FAM193B,IDUA,JMJD7-PLA2G4B,
PIDD1,MICALL2,MYL5,MZF1,NEIL1,PCSK4,PHF1,
SCNN1D,SNRNP70,TMEM129,TMEM175,UBXN11,WASH7P,ZBTB48
A1BG,B3GAT3,OXLD1,C19orf25,C1orf159,C1orf86,BRAT1,
PPP1R35,C9orf142,EVA1B,IDUA,INO80E,LRRC29,MFSD10,
NME3,NPDC1,PIGQ,PNKP,INAFM1,SIRT6,SNAPC2

ADAMTS13,AGAP4,AHSA2,APBB3,CCDC130,CCNL2,CLK2,
CSAD,FAM193B,GIGYF1,IDUA,INPP5E,MDM4,MZF1,
PAQR6,PILRB,SCX,SGK494,SLC26A1,TMEM175,ZNF692
ADAMTS13,ANAPC2,ANKMY1,ANO8,BAIAP3,ENTHD2,C17orf70,
ABHD16B,HDAC10,IDUA,LRRC24,MAN2C1,MIB2,PCSK4,
POLRMT,SELO,SLC12A9,SPPL2B,TYK2,ZDHHC14,ZNF653
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 IDUA


There's no related Drug.
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Cross referenced IDs for IDUA
* 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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