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 IYD
Basic gene info.Gene symbolIYD
Gene nameiodotyrosine deiodinase
SynonymsC6orf71|DEHAL1|TDH4|dJ422F24.1
CytomapUCSC genome browser: 6q25.1
Genomic locationchr6 :150690027-150725765
Type of geneprotein-coding
RefGenesNM_001164694.1,
NM_001164695.1,NM_203395.2,
Ensembl idENSG00000009765
DescriptionIYD-1iodotyrosine dehalogenase 1
Modification date20141207
dbXrefs MIM : 612025
HGNC : HGNC
Ensembl : ENSG00000009765
HPRD : 16668
Vega : OTTHUMG00000016347
ProteinUniProt: Q6PHW0
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_IYD
BioGPS: 389434
Gene Expression Atlas: ENSG00000009765
The Human Protein Atlas: ENSG00000009765
PathwayNCI Pathway Interaction Database: IYD
KEGG: IYD
REACTOME: IYD
ConsensusPathDB
Pathway Commons: IYD
MetabolismMetaCyc: IYD
HUMANCyc: IYD
RegulationEnsembl's Regulation: ENSG00000009765
miRBase: chr6 :150,690,027-150,725,765
TargetScan: NM_001164694
cisRED: ENSG00000009765
ContextiHOP: IYD
cancer metabolism search in PubMed: IYD
UCL Cancer Institute: IYD
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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

check002.gifOthers
OMIM 274800; phenotype.
274800; phenotype.
612025; gene.
612025; gene.
Orphanet 95716; Familial thyroid dyshormonogenesis.
95716; Familial thyroid dyshormonogenesis.
DiseaseKEGG Disease: IYD
MedGen: IYD (Human Medical Genetics with Condition)
ClinVar: IYD
PhenotypeMGI: IYD (International Mouse Phenotyping Consortium)
PhenomicDB: IYD

Mutations for IYD
* 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
ovaryIYDchr6150714242150714262chr6150737579150737599
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 IYD related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG949184NOLC11333810103920547103921646IYD3193876150713521150713589

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            1   
GAIN (# sample)1            1   
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=31)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=1)
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
chr6:150690236-150690236p.A23A3
chr6:150713566-150713566p.I152I3
chr6:150719261-150719261p.R253H2
chr6:150715310-150715310p.A202A2
chr6:150710576-150710576p.R89R2
chr6:150690282-150690282p.E39K2
chr6:150710610-150710610p.R101W2
chr6:150710649-150710649p.E114K2
chr6:150690289-150690289p.R41H2
chr6:150710674-150710674p.T122M1

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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
# sample22 9    2  122  102 8
# mutation22 8    2  122  102 9
nonsynonymous SNV21 8    2   22  81 5
synonymous SNV 1 1       1    21 4
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
chr6:150713566p.I152M,IYD3
chr6:150690236p.R101W,IYD2
chr6:150713632p.A23A,IYD2
chr6:150710610p.E39K,IYD2
chr6:150690282p.K174K,IYD2
chr6:150719329p.A10V,IYD1
chr6:150690205p.P75T,IYD1
chr6:150690326p.R253H1
chr6:150713596p.C13S,IYD1
chr6:150710499p.P264L1

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 IYD 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 IYD

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

ACSM3,AKR1B15,EYS,FDFT1,HS3ST5,IDI1,ISX,
IYD,KLF17,KPNA7,LOC255167,ME1,MECOM,NIPAL2,
SC5D,SLC2A14,SPINK8,TMEM86A,TRIM68,VSX2,WDR64
ABCC12,ADCY10,AKR1D1,ALOX15B,C15orf43,CTNNA2,DDC,
ELOVL7,EPS8L3,FADS2,HIST1H2AG,IDI1,IYD,LST-3TM12,
RIMS1,SERHL,SGPP2,SLC12A3,SLC26A6,TMPRSS11F,ZP2

ARFGEF2,ATP9A,CCDC122,CDH1,COG6,ELF1,FARP1,
IYD,GPALPP1,LRRC2,NAALADL2,NEBL,PIBF1,TGOLN2,
TM9SF2,TMTC4,UBL3,UTP14C,VAV3,VPS36,ZDHHC9
ALPI,SOWAHA,BEND7,TMEM253,CDHR5,CES2,CHN2,
CYP2J2,DEGS2,DGAT1,INPP5J,IYD,MACC1,MEP1A,
MYO1A,NAGS,OIT3,PCK2,SLC22A4,SLC39A5,TM4SF5
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 IYD
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA162392352; -.
Organism-specific databasesPharmGKB PA162392352; -.
Organism-specific databasesCTD 389434; -.
Organism-specific databasesCTD 389434; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB03374iodotyrosine deiodinaseexperimental3,5-Diiodotyrosine


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Cross referenced IDs for IYD
* 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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