Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 HAO2
Basic gene info.Gene symbolHAO2
Gene namehydroxyacid oxidase 2 (long chain)
SynonymsGIG16|HAOX2
CytomapUCSC genome browser: 1p13.3-p13.1
Genomic locationchr1 :119911401-119936751
Type of geneprotein-coding
RefGenesNM_001005783.2,
NM_016527.3,
Ensembl idENSG00000116882
Description(S)-2-hydroxy-acid oxidase, peroxisomalcell growth-inhibiting gene 16 proteinglycolate oxidasehydroxyacid oxidase 2long chain alpha-hydroxy acid oxidaselong-chain L-2-hydroxy acid oxidase
Modification date20141211
dbXrefs MIM : 605176
HGNC : HGNC
Ensembl : ENSG00000116882
HPRD : 05532
Vega : OTTHUMG00000012410
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HAO2
BioGPS: 51179
Gene Expression Atlas: ENSG00000116882
The Human Protein Atlas: ENSG00000116882
PathwayNCI Pathway Interaction Database: HAO2
KEGG: HAO2
REACTOME: HAO2
ConsensusPathDB
Pathway Commons: HAO2
MetabolismMetaCyc: HAO2
HUMANCyc: HAO2
RegulationEnsembl's Regulation: ENSG00000116882
miRBase: chr1 :119,911,401-119,936,751
TargetScan: NM_001005783
cisRED: ENSG00000116882
ContextiHOP: HAO2
cancer metabolism search in PubMed: HAO2
UCL Cancer Institute: HAO2
Assigned class in ccmGDBC

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Phenotypic Information for HAO2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HAO2
Familial Cancer Database: HAO2
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HAO2
MedGen: HAO2 (Human Medical Genetics with Condition)
ClinVar: HAO2
PhenotypeMGI: HAO2 (International Mouse Phenotyping Consortium)
PhenomicDB: HAO2

Mutations for HAO2
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
pancreasHAO2chr1119917280119917300chr46228374762283767
pancreasHAO2chr1119917290119917290chr46228375862283758
pancreasHAO2chr1119920408119920428HAO2chr1119922878119922898
pancreasHAO2chr1119930995119931015HAO2chr1119930910119930930
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 HAO2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI110601RECQL1180122165412021654546HAO21755381119928261119928624
AF062709RECQL1180122165412021654546HAO21755381119928261119928624
BI759383HAO211601119935247119941320HAO21605791119934732119936597

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      2   
GAIN (# sample)      1      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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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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=51)
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
chr1:119936413-119936413p.R336W3
chr1:119936414-119936414p.R336Q3
chr1:119927624-119927624p.R170Q3
chr1:119925542-119925542p.R46C3
chr1:119925543-119925543p.R46H2
chr1:119929330-119929330p.R216Q2
chr1:119925552-119925552p.P49L2
chr1:119934795-119934795p.G278G2
chr1:119927668-119927668p.P185S2
chr1:119927408-119927408p.A98V2

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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
# sample21 61 1 2  7 2  143 11
# mutation21 51 1 2  12 1  173 12
nonsynonymous SNV21 51 1    9 1  93 11
synonymous SNV   1    2  3    8  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
chr1:119936413p.R336W,HAO24
chr1:119923746p.A13V,HAO23
chr1:119923812p.R35L,HAO22
chr1:119923749p.R14L,HAO22
chr1:119927408p.A98V,HAO22
chr1:119927487p.T105T,HAO21
chr1:119923779p.V264M,HAO21
chr1:119929411p.A41S,HAO21
chr1:119925619p.G123S,HAO21
chr1:119936448p.K271N,HAO21

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 HAO2 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 HAO2

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

AKR7A2P1,APLP1,C9orf135,CADPS,DKFZP434H168,DYTN,FGF12,
FLJ46111,GRIA1,GRIN1,HAO2,HDC,KIRREL3,NDP,
PPP1R1C,SEMA6D,SNAP91,TAGLN3,TNNI3K,TPH2,TWISTNB
ATAD2,CDH7,DCAF4L2,GAD1,GUCY1B2,HAO2,HIST1H4L,
IFITM5,KCNU1,KRT26,LRRC31,MAGEC2,MMP20,RLN2,
ROBO2,SLC22A1,SNORA4,SOX14,STXBP5L,TEX14,ZPLD1

AKR1C3,AKR1C4,BST1,CLN5,CST1,CST4,DEFB104A,
ENPP2,HAO2,KL,LRRC69,LRRN3,MAL2,MED4,
MT3,N6AMT2,OR10X1,S100Z,TEKT4,TPT1,UNC5D
BST1,CRYAA,DACH1,GATA4,GGT3P,GGTLC1,HAO2,
HEATR4,HTR4,KCNK17,LCT,LEMD1,PAEP,PDIA2,
ProSAPiP1,RGS7BP,SFTA3,SLC34A2,SNORA80E,TBX18,TMPRSS11D
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 HAO2


There's no related Drug.
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Cross referenced IDs for HAO2
* 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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