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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for HGD |
Basic gene info. | Gene symbol | HGD |
Gene name | homogentisate 1,2-dioxygenase | |
Synonyms | AKU|HGO | |
Cytomap | UCSC genome browser: 3q13.33 | |
Genomic location | chr3 :120347014-120401418 | |
Type of gene | protein-coding | |
RefGenes | NM_000187.3, | |
Ensembl id | ENSG00000113924 | |
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 | ||
Gene Expression Atlas: ENSG00000113924 | ||
The Human Protein Atlas: ENSG00000113924 | ||
Pathway | NCI Pathway Interaction Database: HGD | |
KEGG: HGD | ||
REACTOME: HGD | ||
ConsensusPathDB | ||
Pathway Commons: HGD | ||
Metabolism | MetaCyc: HGD | |
HUMANCyc: HGD | ||
Regulation | Ensembl's Regulation: ENSG00000113924 | |
miRBase: chr3 :120,347,014-120,401,418 | ||
TargetScan: NM_000187 | ||
cisRED: ENSG00000113924 | ||
Context | iHOP: HGD | |
cancer metabolism search in PubMed: HGD | ||
UCL Cancer Institute: HGD | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for HGD(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: HGD |
Familial Cancer Database: HGD |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
KEGG_TYROSINE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: HGD |
MedGen: HGD (Human Medical Genetics with Condition) | |
ClinVar: HGD | |
Phenotype | MGI: HGD (International Mouse Phenotyping Consortium) |
PhenomicDB: HGD |
Mutations for HGD |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HGD related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
DW417230 | NFS1 | 17 | 107 | 20 | 34276829 | 34276919 | HGD | 106 | 134 | 3 | 120389826 | 120389861 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   |   |   | 2 |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   | 2 |   |   |   |   |   |   |   |   | |||
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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=43) | (# total SNVs=16) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr3:120371463-120371463 | p.S106S | 4 |
chr3:120347258-120347258 | p.P436L | 2 |
chr3:120389386-120389386 | p.? | 2 |
chr3:120365209-120365209 | p.G185V | 2 |
chr3:120363206-120363206 | p.V245A | 2 |
chr3:120360505-120360505 | p.G270G | 2 |
chr3:120393784-120393784 | p.S47L | 2 |
chr3:120357386-120357386 | p.P308S | 2 |
chr3:120365150-120365150 | p.G205S | 2 |
chr3:120357389-120357389 | p.R307C | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   | 2 | 1 | 7 |   |   | 3 |   | 2 | 1 |   | 5 | 5 |   |   |   | 19 | 6 | 1 | 8 |
# mutation |   | 2 | 1 | 7 |   |   | 3 |   | 2 | 1 |   | 5 | 5 |   |   |   | 22 | 7 | 1 | 8 |
nonsynonymous SNV |   | 1 | 1 | 6 |   |   | 2 |   | 2 | 1 |   | 4 | 4 |   |   |   | 11 | 3 | 1 | 6 |
synonymous SNV |   | 1 |   | 1 |   |   | 1 |   |   |   |   | 1 | 1 |   |   |   | 11 | 4 |   | 2 |
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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr3:120363206 | p.G270G | 2 |
chr3:120360505 | p.V245A | 2 |
chr3:120347285 | p.R58I | 1 |
chr3:120365144 | p.W427L | 1 |
chr3:120352144 | p.A311A | 1 |
chr3:120371457 | p.H207Y | 1 |
chr3:120360515 | p.N56D | 1 |
chr3:120393830 | p.K414N | 1 |
chr3:120347323 | p.R307H | 1 |
chr3:120365162 | p.L201V | 1 |
Other DBs for Point Mutations |
Copy Number for HGD 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 HGD |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
ABCA12,ARHGEF38,FAH,G6PD,GPR39,GTF2E1,HGD, ME1,MPV17L,NDUFB4,NEK6,ECI2,RABL3,REEP5, SAR1B,SPINK8,TC2N,TMEM62,TMEM86A,TTC1,YIPF1 | AKR1A1,ALDH3B2,CAPN13,GGTLC2,GUSB,HGD,HIST1H2AE, HIST1H2BG,HIST1H3D,HIST1H4H,HRASLS2,LOC145837,MOGAT2,SLC50A1, REEP6,SERHL2,SRD5A1,STYK1,TMEM45B,TMEM63C,UGT2B11 | ||||
A4GNT,ASIC3,ANXA10,APOBEC1,BCAR4,BTBD16,CDS1, CIB1,COX8C,CPS1,EGLN3,FUT2,GATA4,HGD, KCNE3,KLHDC7A,LIPC,LRRC66,PDZK1,WFDC2,ZG16 | C1orf21,VWA7,CCDC152,CDR2,CHRNA7,ELOVL7,GAL3ST1, HGD,LGALS2,LOC146336,MLXIPL,PLLP,SCT,SEPP1, SLC13A2,SLC30A2,SLC37A4,SMPD3,SSTR5,TM4SF5,TMPRSS7 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for HGD |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00143 | homogentisate 1,2-dioxygenase | approved; nutraceutical | Glutathione | ||
DB00120 | homogentisate 1,2-dioxygenase | approved; nutraceutical | L-Phenylalanine | ||
DB00135 | homogentisate 1,2-dioxygenase | approved; nutraceutical | L-Tyrosine | ||
DB00360 | homogentisate 1,2-dioxygenase | approved; investigational | Tetrahydrobiopterin |
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Cross referenced IDs for HGD |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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