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 HAO1
Basic gene info.Gene symbolHAO1
Gene namehydroxyacid oxidase (glycolate oxidase) 1
SynonymsGOX|GOX1|HAOX1
CytomapUCSC genome browser: 20p12
Genomic locationchr20 :7863630-7921093
Type of geneprotein-coding
RefGenesNM_017545.2,
Ensembl idENSG00000101323
Description(S)-2-hydroxy-acid oxidaseglycolate oxidasehydroxyacid oxidase 1
Modification date20141207
dbXrefs MIM : 605023
HGNC : HGNC
Ensembl : ENSG00000101323
HPRD : 05429
Vega : OTTHUMG00000031841
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HAO1
BioGPS: 54363
Gene Expression Atlas: ENSG00000101323
The Human Protein Atlas: ENSG00000101323
PathwayNCI Pathway Interaction Database: HAO1
KEGG: HAO1
REACTOME: HAO1
ConsensusPathDB
Pathway Commons: HAO1
MetabolismMetaCyc: HAO1
HUMANCyc: HAO1
RegulationEnsembl's Regulation: ENSG00000101323
miRBase: chr20 :7,863,630-7,921,093
TargetScan: NM_017545
cisRED: ENSG00000101323
ContextiHOP: HAO1
cancer metabolism search in PubMed: HAO1
UCL Cancer Institute: HAO1
Assigned class in ccmGDBC

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Phenotypic Information for HAO1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HAO1
Familial Cancer Database: HAO1
* 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
KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HAO1
MedGen: HAO1 (Human Medical Genetics with Condition)
ClinVar: HAO1
PhenotypeMGI: HAO1 (International Mouse Phenotyping Consortium)
PhenomicDB: HAO1

Mutations for HAO1
* 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
pancreasHAO1chr2079023587902378HAO1chr2079029057902925
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 HAO1 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 1     1 1
GAIN (# sample)        1     1 1
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=59)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr20:7864254-7864254p.V367F4
chr20:7894923-7894923p.R145W3
chr20:7915169-7915169p.R84H2
chr20:7864303-7864303p.Q350H2
chr20:7895041-7895041p.M105I2
chr20:7886880-7886880p.D214E2
chr20:7866189-7866189p.R341W2
chr20:7915149-7915149p.E91K2
chr20:7921052-7921052p.I6M2
chr20:7894842-7894842p.R172C2

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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
# sample141122 7   11063 179 4
# mutation141102 7   11063 169 4
nonsynonymous SNV14162 5    763 154 4
synonymous SNV   4  2   13    15  
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
chr20:7894842p.R172C3
chr20:7895041p.M105I2
chr20:7875841p.V360M1
chr20:7915243p.D291D1
chr20:7864275p.A207T1
chr20:7886903p.A81A1
chr20:7866404p.R341R1
chr20:7895057p.V282V1
chr20:7875859p.D201Y1
chr20:7915256p.S72I1

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 HAO1 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 HAO1

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

ANXA2P3,LINC00479,CLDN6,DTD1,HAO1,HFM1,KRTAP2-1,
KRTAP2-2,LECT1,LOC340094,LINC00493,MATN4,LINC00112,LINC00113,
OR10W1,POLR3F,SNRPB2,SPTA1,SUGT1,TM2D2,ZIC3
GLIS3-AS1,ERAS,F2RL2,FAM136A,FAM138E,EVA1A,FMO1,
FZD10,HAO1,LOC282997,MAGED4,MIR503HG,NRXN2,OBP2A,
PSD,SAAL1,SCG5,TBC1D7,TCEAL5,TMEM158,XPNPEP1

CRCT1,CRNN,HAO1,IL36A,KRT14,KRT6A,KRT6C,
KRT78,CERS3,LCE3D,LCE3E,MRGPRX3,SBSN,SDR9C7,
SERPINB13,SPRR2A,SPRR2B,SPRR2C,SPRR2E,TGM1,TMPRSS11F
ALB,APCS,APOA2,C3P1,C8A,CFHR2,CFHR5,
CYP4A22,DNAJB8,F13B,F9,FGG,HAO1,KIR3DP1,
KRTAP4-11,KRTAP5-3,LECT2,LOC100129935,LINC00160,OR1N1,SLC17A2
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 HAO1
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
DB02164hydroxyacid oxidase (glycolate oxidase) 1experimentalN-Sulfo-Flavin Mononucleotide
DB02279hydroxyacid oxidase (glycolate oxidase) 1experimentalBenzoylformic Acid
DB03014hydroxyacid oxidase (glycolate oxidase) 1experimentalHeme
DB03064hydroxyacid oxidase (glycolate oxidase) 1experimental3-Decyl-2,5-Dioxo-4-Hydroxy-3-Pyrroline
DB03247hydroxyacid oxidase (glycolate oxidase) 1experimentalRiboflavin Monophosphate
DB03884hydroxyacid oxidase (glycolate oxidase) 1experimental3-Phenylpyruvic Acid
DB04374hydroxyacid oxidase (glycolate oxidase) 1experimental4-Carboxy-5-(1-Pentyl)Hexylsulfanyl-1,2,3-Triazole
DB06979hydroxyacid oxidase (glycolate oxidase) 1experimental5-(dodecylthio)-1H-1,2,3-triazole-4-carboxylic acid
DB07060hydroxyacid oxidase (glycolate oxidase) 1experimental3-(INDOL-3-YL) LACTATE
DB07907hydroxyacid oxidase (glycolate oxidase) 1experimental(2S)-2-HYDROXYOCTANOIC ACID
DB00145hydroxyacid oxidase (glycolate oxidase) 1approved; nutraceuticalGlycine
DB00160hydroxyacid oxidase (glycolate oxidase) 1approved; nutraceuticalL-Alanine


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Cross referenced IDs for HAO1
* 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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