Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	HAO2
	Gene name	hydroxyacid oxidase 2 (long chain)
	Synonyms	GIG16\|HAOX2
	Cytomap	UCSC genome browser: 1p13.3-p13.1
	Genomic location	chr1 :119911401-119936751
	Type of gene	protein-coding
	RefGenes	NM_001005783.2, NM_016527.3,
	Ensembl id	ENSG00000116882
	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 date	20141211
dbXrefs	MIM : 605176
	HGNC : HGNC
	Ensembl : ENSG00000116882
	HPRD : 05532
	Vega : OTTHUMG00000012410
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HAO2
	BioGPS: 51179
	Gene Expression Atlas: ENSG00000116882
	The Human Protein Atlas: ENSG00000116882
Pathway	NCI Pathway Interaction Database: HAO2
	KEGG: HAO2
	REACTOME: HAO2
	ConsensusPathDB
	Pathway Commons: HAO2
Metabolism	MetaCyc: HAO2
	HUMANCyc: HAO2
Regulation	Ensembl's Regulation: ENSG00000116882
	miRBase: chr1 :119,911,401-119,936,751
	TargetScan: NM_001005783
	cisRED: ENSG00000116882
Context	iHOP: HAO2
	cancer metabolism search in PubMed: HAO2
	UCL Cancer Institute: HAO2
Assigned class in ccmGDB	C

Top

Phenotypic Information for HAO2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: HAO2
	MedGen: HAO2 (Human Medical Genetics with Condition)
	ClinVar: HAO2
Phenotype	MGI: HAO2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

Top

- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	HAO2	chr1	119917280	119917300		chr4	62283747	62283767
pancreas	HAO2	chr1	119917290	119917290		chr4	62283758	62283758
pancreas	HAO2	chr1	119920408	119920428	HAO2	chr1	119922878	119922898
pancreas	HAO2	chr1	119930995	119931015	HAO2	chr1	119930910	119930930

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HAO2 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
AI110601	RECQL	1	180	12	21654120	21654546	HAO2	175	538	1	119928261	119928624
AF062709	RECQL	1	180	12	21654120	21654546	HAO2	175	538	1	119928261	119928624
BI759383	HAO2	1	160	1	119935247	119941320	HAO2	160	579	1	119934732	119936597

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

Top

SNV 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

Top

Somatic 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.

Top

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
chr1:119925542-119925542	p.R46C	3
chr1:119936413-119936413	p.R336W	3
chr1:119927624-119927624	p.R170Q	3
chr1:119936414-119936414	p.R336Q	3
chr1:119934795-119934795	p.G278G	2
chr1:119927668-119927668	p.P185S	2
chr1:119927408-119927408	p.A98V	2
chr1:119936434-119936434	p.R343*	2
chr1:119927551-119927551	p.E146Q	2
chr1:119934803-119934803	p.R281Q	2

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2	1		6	1		1		2			7		2			14	3		11
# mutation	2	1		5	1		1		2			12		1			17	3		12
nonsynonymous SNV	2	1		5	1		1					9		1			9	3		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])

Top

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
chr1:119936413	p.R336W,HAO2	4
chr1:119923746	p.A13V,HAO2	3
chr1:119923812	p.R14L,HAO2	2
chr1:119923749	p.A98V,HAO2	2
chr1:119927408	p.R35L,HAO2	2
chr1:119925635	p.E57A,HAO2	1
chr1:119927555	p.I142I,HAO2	1
chr1:119934751	p.V58V,HAO2	1
chr1:119925636	p.S147F,HAO2	1
chr1:119923714	p.A339S,HAO2	1

Other 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

Copy 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]

Top

Gene Expression for HAO2

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for HAO2

There's no related Drug.

Top

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