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 HAL
Basic gene info.Gene symbolHAL
Gene namehistidine ammonia-lyase
SynonymsHIS|HSTD
CytomapUCSC genome browser: 12q22-q24.1
Genomic locationchr12 :96366439-96390143
Type of geneprotein-coding
RefGenesNM_001258333.1,
NM_001258334.1,NM_002108.3,
Ensembl idENSG00000084110
Descriptionhistidase
Modification date20141207
dbXrefs MIM : 609457
HGNC : HGNC
Ensembl : ENSG00000084110
HPRD : 07187
Vega : OTTHUMG00000170354
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HAL
BioGPS: 3034
Gene Expression Atlas: ENSG00000084110
The Human Protein Atlas: ENSG00000084110
PathwayNCI Pathway Interaction Database: HAL
KEGG: HAL
REACTOME: HAL
ConsensusPathDB
Pathway Commons: HAL
MetabolismMetaCyc: HAL
HUMANCyc: HAL
RegulationEnsembl's Regulation: ENSG00000084110
miRBase: chr12 :96,366,439-96,390,143
TargetScan: NM_001258333
cisRED: ENSG00000084110
ContextiHOP: HAL
cancer metabolism search in PubMed: HAL
UCL Cancer Institute: HAL
Assigned class in ccmGDBC

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

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

Mutations for HAL
* 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 HAL 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 # sample1     2          
GAIN (# sample)                 
LOSS (# sample)1     2          
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=66)
Stat. for Synonymous SNVs
(# total SNVs=13)
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
chr12:96368029-96368029p.P652L3
chr12:96379724-96379724p.R390C3
chr12:96379885-96379885p.R369W3
chr12:96389483-96389483p.R69Q3
chr12:96374435-96374435p.R473L3
chr12:96384198-96384198p.P276P2
chr12:96374458-96374458p.A465A2
chr12:96380970-96380970p.T309M2
chr12:96389601-96389601p.E30K2
chr12:96370239-96370239p.E601K2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample42 132 2 1  322  163 8
# mutation42 132 2 1  322  163 9
nonsynonymous SNV22 92 2 1  321  92 6
synonymous SNV2  4         1  71 3
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
chr12:96384198p.R192L,HAL2
chr12:96387243p.R360C,HAL2
chr12:96370437p.P68P,HAL2
chr12:96368029p.P38S,HAL1
chr12:96384181p.F53F,HAL1
chr12:96387882p.R386C,HAL1
chr12:96370474p.G228V,HAL1
chr12:96389549p.P204P,HAL1
chr12:96377755p.V48M,HAL1
chr12:96368046p.V371V,HAL1

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 HAL 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 HAL

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

APOA1,APOB,ARG1,C3P1,CA5A,COLEC11,CREB3L3,
CYP8B1,FABP1,GCKR,HAL,HP,ITIH3,LOC285733,
LOC55908,MT1DP,SERPINA10,SLC17A2,SLC2A2,SULT2A1,TM4SF5
ACSM2A,ACSM2B,AMN,APOC3,APOL4,TBATA,CHGA,
DBH,GLYCTK,HAL,NDRG4,NTSR2,ORM1,ORM2,
PDZD7,PHOX2B,RASL10B,SNORA14A,ST8SIA3,TAGLN3,TH

ABRA,ADAMTS16,C14orf132,CSPG4,FAM135B,FLNC,GFAP,
GJC1,GKN2,HAL,HSPB7,ITGB3,LOC100132111,MORC1,
NRG1,OR2T4,PABPC1L2B,PENK,SLC26A9,VAT1L,WSCD2
ARL15,LSMEM1,C8orf34,CSN1S1,DTWD2,FAM13A-AS1,FAM91A1,
FAR1,FASTKD1,GEN1,HAL,LOC440944,PFKFB2,PIWIL4,
SLC19A2,SNHG12,SPAST,TRPM7,TTC19,USP45,ZNF600
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 HAL
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
DB00117histidine ammonia-lyaseapproved; nutraceuticalL-Histidine
DB06946histidine ammonia-lyaseexperimental(2S,3S)-3-(4-fluorophenyl)-2,3-dihydroxypropanoic acid
DB01880histidine ammonia-lyaseexperimental3,4-Dihydroxycinnamic Acid
DB04066histidine ammonia-lyaseexperimentalPara-Coumaric Acid


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Cross referenced IDs for HAL
* 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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