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 GLA
Basic gene info.Gene symbolGLA
Gene namegalactosidase, alpha
SynonymsGALA
CytomapUCSC genome browser: Xq22
Genomic locationchrX :100652778-100663001
Type of geneprotein-coding
RefGenesNM_000169.2,
Ensembl idENSG00000268815
Descriptionagalsidase alfaalpha-D-galactosidase Aalpha-D-galactoside galactohydrolase 1alpha-gal Aalpha-galactosidase Amelibiase
Modification date20141219
dbXrefs MIM : 300644
HGNC : HGNC
Ensembl : ENSG00000102393
HPRD : 02357
Vega : OTTHUMG00000022026
ProteinUniProt: P06280
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GLA
BioGPS: 2717
Gene Expression Atlas: ENSG00000268815
The Human Protein Atlas: ENSG00000268815
PathwayNCI Pathway Interaction Database: GLA
KEGG: GLA
REACTOME: GLA
ConsensusPathDB
Pathway Commons: GLA
MetabolismMetaCyc: GLA
HUMANCyc: GLA
RegulationEnsembl's Regulation: ENSG00000268815
miRBase: chrX :100,652,778-100,663,001
TargetScan: NM_000169
cisRED: ENSG00000268815
ContextiHOP: GLA
cancer metabolism search in PubMed: GLA
UCL Cancer Institute: GLA
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GLA(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GLA
Familial Cancer Database: GLA
* 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_GALACTOSE_METABOLISM
KEGG_GLYCEROLIPID_METABOLISM
KEGG_SPHINGOLIPID_METABOLISM
REACTOME_GLYCOSPHINGOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 300644; gene.
301500; phenotype.
Orphanet 324; Fabry disease.
DiseaseKEGG Disease: GLA
MedGen: GLA (Human Medical Genetics with Condition)
ClinVar: GLA
PhenotypeMGI: GLA (International Mouse Phenotyping Consortium)
PhenomicDB: GLA

Mutations for GLA
* 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 GLA 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
There's no copy number variation information in COSMIC data for this gene.

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=44)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr23:100652899-100652899p.F396L2
chr23:100656792-100656792p.H125Q2
chr23:100652895-100652895p.E398Q1
chr23:100658838-100658838p.P110P1
chr23:100653459-100653459p.L300F1
chr23:100662735-100662735p.N53Y1
chr23:100655659-100655659p.Q212E1
chr23:100658854-100658854p.R105K1
chr23:100653510-100653510p.Q283*1
chr23:100662741-100662741p.M51V1

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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
# sample 216  2 2  64   12 8
# mutation 217  2 2  64   12 10
nonsynonymous SNV 216  2 2  53   1  7
synonymous SNV   1       11    2 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
chrX:100652899p.F396L2
chrX:100653447p.V281V1
chrX:100656651p.R105K1
chrX:100658904p.N278K1
chrX:100653459p.E103D1
chrX:100656666p.P265Q1
chrX:100658929p.Q99K1
chrX:100653514p.E251E1
chrX:100656686p.D93H1
chrX:100662699p.W236C1

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 GLA 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 GLA

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

ARMCX1,ARMCX3,CLIC6,CYP2C8,FUT8,GLA,GLUL,
HNRNPH2,LOC645431,LRIG1,MREG,MYB,MYBPC1,NMUR2,
NXNL2,PDCD4,PTHLH,RUNX1,SEMA3C,SGK223,TMEM26
ACMSD,AGR3,CLPSL2,CHST8,DEGS2,GLA,HSPA5,
KCNK6,MTFP1,LINC00160,NLRP5,PVRL2,SCARNA22,SEC14L2,
SERPINA11,SERPINA1,SERPINA3,SIAH2,SLC9A3R1,SNORA78,TMC3

APEX2,CXorf40B,EMD,FTSJ1,GLA,HDAC8,LAS1L,
MORF4L2,NAA10,NKRF,NSDHL,PDZD11,PRPS1,RBMX2,
SLC25A14,SLC25A5,SUV39H1,TIMM8A,UBE2A,UBL4A,VBP1
ABHD6,AKR1A1,ANPEP,ANXA4,APOBEC1,ARG2,FUOM,
TMEM256,RTCB,IDNK,CA13,CBR1,FAM3B,GCHFR,
GK,GK3P,GLA,GLRX,GOLT1A,HOXC9,MOCOS
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 GLA
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P06280; -.
ChemistryChEMBL CHEMBL2524; -.
Organism-specific databasesPharmGKB PA28707; -.
Organism-specific databasesCTD 2717; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02944galactosidase, alphaexperimentalAlpha-D-Mannose


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Cross referenced IDs for GLA
* 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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