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 DIO2
Basic gene info.Gene symbolDIO2
Gene namedeiodinase, iodothyronine, type II
Synonyms5DII|D2|DIOII|SelY|TXDI2
CytomapUCSC genome browser: 14q24.2-q24.3
Genomic locationchr14 :80663867-80677864
Type of geneprotein-coding
RefGenesNM_000793.5,
NM_001007023.3,NM_001242502.1,NM_001242503.1,NM_013989.4,
Ensembl idENSG00000211448
Descriptiondeiodinase-2deiodonase-2thyroxine deiodinase, type IItype 2 DItype 2 iodothyronine deiodinasetype II iodothyronine deiodinasetype-II 5'-deiodinasetype-II 5'deiodinase
Modification date20141207
dbXrefs MIM : 601413
HGNC : HGNC
Ensembl : ENSG00000211448
HPRD : 09027
Vega : OTTHUMG00000171443
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DIO2
BioGPS: 1734
Gene Expression Atlas: ENSG00000211448
The Human Protein Atlas: ENSG00000211448
PathwayNCI Pathway Interaction Database: DIO2
KEGG: DIO2
REACTOME: DIO2
ConsensusPathDB
Pathway Commons: DIO2
MetabolismMetaCyc: DIO2
HUMANCyc: DIO2
RegulationEnsembl's Regulation: ENSG00000211448
miRBase: chr14 :80,663,867-80,677,864
TargetScan: NM_000793
cisRED: ENSG00000211448
ContextiHOP: DIO2
cancer metabolism search in PubMed: DIO2
UCL Cancer Institute: DIO2
Assigned class in ccmGDBC

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Phenotypic Information for DIO2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DIO2
Familial Cancer Database: DIO2
* 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: DIO2
MedGen: DIO2 (Human Medical Genetics with Condition)
ClinVar: DIO2
PhenotypeMGI: DIO2 (International Mouse Phenotyping Consortium)
PhenomicDB: DIO2

Mutations for DIO2
* 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 DIO2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample        1        
GAIN (# sample)                 
LOSS (# sample)        1        
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=41)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr14:80669227-80669227p.R209R2
chr14:80669424-80669424p.R144S2
chr14:80669148-80669148p.Q236K2
chr14:80669428-80669428p.A142A2
chr14:80669184-80669184p.G224R2
chr14:80669394-80669394p.A154S2
chr14:80669111-80669111p.S248F2
chr14:80669601-80669601p.S85G2
chr14:80669412-80669412p.E148K1
chr14:80669126-80669126p.G243E1

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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
# sample1  1       52    2 1
# mutation1  1       62    2 1
nonsynonymous SNV           52    2 1
synonymous SNV1  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
chr14:80677716p.L34F2
chr14:80677658p.R53P2
chr14:80677661p.T47N1
chr14:80677662p.L41F1
chr14:80677673p.V31V1
chr14:80677676p.L100L1
chr14:80677693p.V63D1
chr14:80672001p.V63F1
chr14:80677723p.R53R1
chr14:80677628p.R52L1

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 DIO2 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 DIO2

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

ABCC2,ABCC3,CEP128,C2CD4A,CA10,CELP,COL6A5,
CXCL6,DENND4C,DIO2,ERO1L,FMO1,FOCAD,LINC01105,
MAGEC1,MBNL3,MS4A10,PIAS1,PVRL3,SNAR-B2,TMEM45B
AMPH,CALML3,CDSN,CWH43,CXCL6,CYP4F22,DIO2,
DNAJB3,FAM177B,FOXL2,HMGB4,KRTAP15-1,LOC286359,MEPE,
OR10G8,OR4P4,PNMT,PTHLH,SLC18A3,TNFSF11,WNT4

ANTXR1,BICC1,CNTN4,COL8A2,CPZ,CTSK,DIO2,
EVC,FAM19A5,FIBIN,FZD1,GLI1,GLIS2,HMCN1,
ISLR,ITGBL1,MXRA8,OLFML1,OLFML2B,OMD,SSPN
ALOX15B,ANTXRL,C11orf42,C15orf43,CA5A,CDK6,CMTM4,
DIO2,GLI1,HHIP,HUNK,KREMEN1,CERS6,LOC150185,
MC3R,OR1L6,PTCH1,ROPN1,SCNN1B,SDHAP2,WNT2B
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 DIO2
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 IIapprovedLevothyroxine


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Cross referenced IDs for DIO2
* 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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