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 DIO1
Basic gene info.Gene symbolDIO1
Gene namedeiodinase, iodothyronine, type I
Synonyms5DI|TXDI1
CytomapUCSC genome browser: 1p33-p32
Genomic locationchr1 :54359860-54376759
Type of geneprotein-coding
RefGenesNM_000792.5,
NM_001039715.1,NM_001039716.1,NM_213593.3,
Ensembl idENSG00000211452
DescriptionDIOIiodothyronine deiodinase type 1thyroxine deiodinase type I (selenoprotein)type 1 DItype I iodothyronine deiodinasetype-I 5'-deiodinase
Modification date20141207
dbXrefs MIM : 147892
HGNC : HGNC
Ensembl : ENSG00000211452
HPRD : 01002
Vega : OTTHUMG00000008435
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DIO1
BioGPS: 1733
Gene Expression Atlas: ENSG00000211452
The Human Protein Atlas: ENSG00000211452
PathwayNCI Pathway Interaction Database: DIO1
KEGG: DIO1
REACTOME: DIO1
ConsensusPathDB
Pathway Commons: DIO1
MetabolismMetaCyc: DIO1
HUMANCyc: DIO1
RegulationEnsembl's Regulation: ENSG00000211452
miRBase: chr1 :54,359,860-54,376,759
TargetScan: NM_000792
cisRED: ENSG00000211452
ContextiHOP: DIO1
cancer metabolism search in PubMed: DIO1
UCL Cancer Institute: DIO1
Assigned class in ccmGDBC

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Phenotypic Information for DIO1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DIO1
Familial Cancer Database: DIO1
* 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
Orphanet
DiseaseKEGG Disease: DIO1
MedGen: DIO1 (Human Medical Genetics with Condition)
ClinVar: DIO1
PhenotypeMGI: DIO1 (International Mouse Phenotyping Consortium)
PhenomicDB: DIO1

Mutations for DIO1
* 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
breastDIO1chr15436942154369421chr15437894454378944
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 DIO1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA641783LOC1005074121106?112074112179DIO110753415435986054370405

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=18)
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
chr1:54359925-54359925p.W14*3
chr1:54360102-54360102p.F73F3
chr1:54375643-54375643p.R193C2
chr1:54359887-54359887p.G2R1
chr1:54371967-54371967p.K179K1
chr1:54360030-54360030p.G49G1
chr1:54371785-54371787p.N120delN1
chr1:54359894-54359894p.P4L1
chr1:54375618-54375618p.P184P1
chr1:54360051-54360051p.F56F1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 4       31   4117
# mutation11 4       31   4116
nonsynonymous SNV   1       2    2115
synonymous SNV11 3       11   2  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
chr1:54360102p.F73F3
chr1:54375643p.R193C2
chr1:54359887p.G2R1
chr1:54360179p.I176I1
chr1:54359913p.L10L1
chr1:54360202p.K179K1
chr1:54360005p.I41N1
chr1:54371825p.P184P1
chr1:54360012p.A43A1
chr1:54371895p.M44T1

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 DIO1 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 DIO1

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

CA12,CHPT1,COQ7,DIO1,GPHN,HSPB8,KRT33A,
KRT37,LRIG1,MCEE,NKIRAS1,PEX12,PEX2,PTGER3,
RMND1,SPCS1,STC2,SYBU,TNK1,TPSG1,WWP1
ASCL2,BAGE,C11orf85,C2orf50,CNTD2,DIO1,GALNTL6,
GATA5,KCNF1,KCNK15,MCHR1,MYT1,NTSR1,OR56A3,
PSCA,SLC7A13,SPANXC,VSTM2A,ABHD11-AS1,WBSCR28,WNT3A

C3P1,CACNG1,ACKR2___ACKR4,CD7,CXorf49B,DIO1,DMRTB1,
FLJ35024,GSTA3,LOC100133669,MS4A15,psiTPTE22,RDH8,RMST,
S100A7A,STOML3,TESK2,TFAP2E,VSIG10L,WIPF3,YBX1
ADORA3,AKR1B1,ALOX15B,ANTXRL,C15orf43,CA5A,DIO1,
ITGA10,KIR2DL3,LILRA2,LOC731789,LY6K,MC3R,MERTK,
NDRG2,OR1L6,P2RY14,SDHAP2,SIGLEC8,SP9,TRMT12
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 DIO1
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
DB00451deiodinase, iodothyronine, type IapprovedLevothyroxine


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Cross referenced IDs for DIO1
* 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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