TissGeneSummary for HGD |
Gene summary |
Basic gene information | Gene symbol | HGD |
Gene name | homogentisate 1,2-dioxygenase | |
Synonyms | AKU|HGO | |
Cytomap | UCSC genome browser: 3q13.33 | |
Type of gene | protein-coding | |
RefGenes | NM_000187.3, | |
Description | homogentisate oxidasehomogentisate oxygenasehomogentisic acid oxidasehomogentisicase | |
Modification date | 20141222 | |
dbXrefs | MIM : 607474 | |
HGNC : HGNC | ||
Ensembl : ENSG00000113924 | ||
HPRD : 06315 | ||
Vega : OTTHUMG00000159441 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_HGD | |
BioGPS: 3081 | ||
Pathway | NCI Pathway Interaction Database: HGD | |
KEGG: HGD | ||
REACTOME: HGD | ||
Pathway Commons: HGD | ||
Context | iHOP: HGD | |
ligand binding site mutation search in PubMed: HGD | ||
UCL Cancer Institute: HGD | ||
Assigned class in TissGDB* | C | |
Included tissue-specific gene expression resources | TiGER,GTEx | |
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | KidneyLiver | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | KIRC,KIRP,KICHLIHC | |
Reference showing the relevant tissue of HGD | ||
Description by TissGene annotations | Protective TissGene in OS |
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO term | PubMed ID |
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TissGeneExp for HGD |
Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01) |
Gene expressions across normal tissues of GTEx data (GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct) - Here, we shows the matched tissue types only among our 28 cancer types. |
Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
THCA | 1.468652537 | 5.020647452 | -3.551994915 | 4.01E-17 | 7.59E-16 |
LUAD | 0.931056073 | -0.973930134 | 1.904986207 | 1.36E-05 | 3.92E-05 |
KICH | 3.052523452 | 5.129987452 | -2.077464 | 6.45E-06 | 2.11E-05 |
LUSC | -3.473446665 | -0.988456469 | -2.484990196 | 3.88E-11 | 1.52E-10 |
COAD | 1.164885914 | 3.163782068 | -1.998896154 | 1.47E-08 | 1.25E-07 |
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TissGene-miRNA for HGD |
Significantly anti-correlated miRNAs of TissGene across 28 cancer types (Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016) (TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21) (TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16) (Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25)) |
Cancer type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
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TissGeneMut for HGD |
TissGeneSNV for HGD |
nsSNV counts per each loci. Different colors of circles represent different cancer types. Circle size denotes number of samples. (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) * Click on the image to enlarge it in a new window. |
Somatic nucleotide variants of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of mutated samples) The numbers in parentheses are numbers of samples with mutation (nsSNVs). (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) |
- nsSNVs sorted by frequency. |
AAchange | Cancer type | # samples |
p.L201V | STAD | 2 |
p.G28E | SKCM | 2 |
p.N56D | LUAD | 1 |
p.I125K | LIHC | 1 |
p.D77N | CESC | 1 |
p.H207Y | COAD | 1 |
p.G185V | LUSC | 1 |
p.Q258_splice | LUSC | 1 |
p.E87K | SKCM | 1 |
p.G23D | LUSC | 1 |
p.Y166H | BLCA | 1 |
p.F282V | UCEC | 1 |
p.W85* | SKCM | 1 |
p.A392T | COAD | 1 |
p.E195D | BLCA | 1 |
p.A381P | COAD | 1 |
p.G394C | LUAD | 1 |
p.G28R | SKCM | 1 |
p.S16L | BLCA | 1 |
p.V284I | SKCM | 1 |
p.N440K | LUSC | 1 |
p.W268X | PAAD | 1 |
p.I246V | UCEC | 1 |
p.H70N | THYM | 1 |
p.N437K | LGG | 1 |
p.S189C | LIHC | 1 |
p.T140A | KIRC | 1 |
p.W268* | PAAD | 1 |
p.N264S | STAD | 1 |
p.P370L | SKCM | 1 |
p.S47L | UCEC | 1 |
p.R58I | COAD | 1 |
p.A267D | UCEC | 1 |
p.D77G | STAD | 1 |
p.P32S | SKCM | 1 |
p.W233R | CESC | 1 |
p.P436L | SKCM | 1 |
p.K414N | COAD | 1 |
p.T369A | SKCM | 1 |
p.D91H | THCA | 1 |
p.P215S | SKCM | 1 |
p.S16L | HNSC | 1 |
p.P158L | LGG | 1 |
p.A442T | SKCM | 1 |
p.D393N | LGG | 1 |
p.S261F | SKCM | 1 |
p.R225C | SKCM | 1 |
p.Y37H | SKCM | 1 |
p.N437K | ACC | 1 |
p.A48T | UCEC | 1 |
p.G170S | ESCA | 1 |
p.S366I | STAD | 1 |
p.V181I | ESCA | 1 |
p.R307H | READ | 1 |
p.F10L | BRCA | 1 |
p.P72S | SKCM | 1 |
p.C377* | LGG | 1 |
p.V245A | UCEC | 1 |
p.S150L | SKCM | 1 |
p.E195D | HNSC | 1 |
p.W85C | LIHC | 1 |
p.I200T | PAAD | 1 |
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TissGeneCNV for HGD |
Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples) (TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16) |
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TissGeneFusions for HGD |
Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
Chimerdb3.0 | ChiTaRs | NA | DW417230 | NFS1-HGD | chr20:34276919 | chr3:120389826 |
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TissGeneNet for HGD |
Co-expressed gene networks based on protein-protein interaction data (CePIN) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (PINA2 ppi data) |
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TissGeneProg for HGD |
Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image to enlarge it in a new window. |
Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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TissGeneClin for HGD |
TissGeneDrug for HGD |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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TissGeneDisease for HGD |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0002066 | Alkaptonuria | 35 | BeFree,CLINVAR,CTD_human,LHGDN,MGD,ORPHANET,UNIPROT |
umls:C0028817 | Ochronosis | 3 | BeFree |
umls:C0001430 | Adenoma | 2 | BeFree |
umls:C0025517 | Metabolic Diseases | 2 | BeFree |
umls:C0001973 | Alcoholic Intoxication, Chronic | 1 | GAD |
umls:C0003864 | Arthritis | 1 | BeFree |
umls:C0009324 | Ulcerative Colitis | 1 | BeFree |
umls:C0025521 | Inborn Errors of Metabolism | 1 | BeFree |
umls:C0032584 | polyps | 1 | BeFree |
umls:C0035078 | Kidney Failure | 1 | BeFree |
umls:C0086543 | Cataract | 1 | BeFree |
umls:C0266929 | Chronic Periodontitis | 1 | BeFree |
umls:C0267375 | Chronic colitis | 1 | BeFree |
umls:C0268493 | Ochronotic arthritis | 1 | BeFree |
umls:C0409224 | Ochronotic arthropathy | 1 | BeFree |
umls:C2931645 | Ochronosis, hereditary | 0 | ORPHANET |