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 HAGH
Basic gene info.Gene symbolHAGH
Gene namehydroxyacylglutathione hydrolase
SynonymsGLO2|GLX2|GLXII|HAGH1
CytomapUCSC genome browser: 16p13.3
Genomic locationchr16 :1859103-1877195
Type of geneprotein-coding
RefGenesNM_001040427.1,
NM_001286249.1,NM_005326.4,
Ensembl idENSG00000063854
Descriptionglx IIglyoxalase IIhydroxyacylglutathione hydrolase, mitochondrialhydroxyacylglutathione hydroxylase
Modification date20141207
dbXrefs MIM : 138760
HGNC : HGNC
HPRD : 00731
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HAGH
BioGPS: 3029
Gene Expression Atlas: ENSG00000063854
The Human Protein Atlas: ENSG00000063854
PathwayNCI Pathway Interaction Database: HAGH
KEGG: HAGH
REACTOME: HAGH
ConsensusPathDB
Pathway Commons: HAGH
MetabolismMetaCyc: HAGH
HUMANCyc: HAGH
RegulationEnsembl's Regulation: ENSG00000063854
miRBase: chr16 :1,859,103-1,877,195
TargetScan: NM_001040427
cisRED: ENSG00000063854
ContextiHOP: HAGH
cancer metabolism search in PubMed: HAGH
UCL Cancer Institute: HAGH
Assigned class in ccmGDBC

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

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

Mutations for HAGH
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HAGH 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          
GAIN (# sample) 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=12)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr16:1866933-1866933p.P188P3
chr16:1872925-1872925p.L16V2
chr16:1867224-1867224p.A149V2
chr16:1872330-1872330p.L47L2
chr16:1859305-1859305p.Q254H1
chr16:1867243-1867243p.K143E1
chr16:1872337-1872338p.V45fs*201
chr16:1859330-1859330p.R246L1
chr16:1869159-1869159p.F118F1
chr16:1872355-1872355p.A39V1

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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
# sample11 11 1 21 1 1  24 1
# mutation11 11 1 21 1 1  24 1
nonsynonymous SNV1   1 1 2  1 1  13  
synonymous SNV 1 1     1      11 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
chr16:1866933p.P200L3
chr16:1872925p.L64V,HAGH2
chr16:1859322p.R170M,HAGH1
chr16:1869997p.R161W,HAGH1
chr16:1859330p.F166F,HAGH1
chr16:1872326p.A154T,HAGH1
chr16:1859771p.L133L,HAGH1
chr16:1872923p.Y124Y,HAGH1
chr16:1866929p.N111N,HAGH1
chr16:1867196p.T97P,HAGH1

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 HAGH 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 HAGH

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

AMDHD2,TSR3,CCDC78,FAM173A,FAM195A,FBXL15,HAGHL,
METRN,MPG,MRPL28,MRPS34,NARFL,NDUFB10,NME3,
NUBP2,PGP,POLR2L,RHOT2,SCAND1,STUB1,TMEM191A
ADCK5,B4GALNT4,C16orf59,CLN6,DCTPP1,FBXL6,FEN1,
GALE,SLC52A2,HAGHL,MAZ,METRN,PAFAH1B3,PAQR4,
PUS1,PYCRL,RECQL4,RHPN1,RNASEH2A,TPRN,TRIM11

ATP5D,ADM5,CCDC78,CSN3,CT47A1,DCDC1,DPP7,
F12,FAM173A,FBXL16,FSCN2,HAGHL,ITGA2B,KCNK7,
KLRC1,KREMEN2,METRN,MT1H,OR6V1,SSPO,STUB1
APBA3,APOBEC3D,C19orf60,PPP1R35,DNAJC4,ABHD17A,FBXL15,
HAGHL,INO80B,LIME1,LRRC26,MUTYH,OGFOD2,PLCB2,
RGS14,SIPA1,TRADD,TSSK6,USF2,ZNF524,ZNF837
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 HAGH
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
DB00143hydroxyacylglutathione hydrolaseapproved; nutraceuticalGlutathione
DB03889hydroxyacylglutathione hydrolaseexperimentalS-(N-Hydroxy-N-Bromophenylcarbamoyl)Glutathione


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Cross referenced IDs for HAGH
* 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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