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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GAA |
Basic gene info. | Gene symbol | GAA |
Gene name | glucosidase, alpha; acid | |
Synonyms | LYAG | |
Cytomap | UCSC genome browser: 17q25.2-q25.3 | |
Genomic location | chr17 :78075354-78093679 | |
Type of gene | protein-coding | |
RefGenes | NM_000152.3, NM_001079803.1,NM_001079804.1, | |
Ensembl id | ENSG00000171298 | |
Description | acid maltaseaglucosidase alfalysosomal alpha-glucosidase | |
Modification date | 20141219 | |
dbXrefs | MIM : 606800 | |
HGNC : HGNC | ||
Ensembl : ENSG00000171298 | ||
HPRD : 06006 | ||
Vega : OTTHUMG00000177537 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GAA | |
BioGPS: 2548 | ||
Gene Expression Atlas: ENSG00000171298 | ||
The Human Protein Atlas: ENSG00000171298 | ||
Pathway | NCI Pathway Interaction Database: GAA | |
KEGG: GAA | ||
REACTOME: GAA | ||
ConsensusPathDB | ||
Pathway Commons: GAA | ||
Metabolism | MetaCyc: GAA | |
HUMANCyc: GAA | ||
Regulation | Ensembl's Regulation: ENSG00000171298 | |
miRBase: chr17 :78,075,354-78,093,679 | ||
TargetScan: NM_000152 | ||
cisRED: ENSG00000171298 | ||
Context | iHOP: GAA | |
cancer metabolism search in PubMed: GAA | ||
UCL Cancer Institute: GAA | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for GAA(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GAA |
Familial Cancer Database: GAA |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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_GALACTOSE_METABOLISM KEGG_STARCH_AND_SUCROSE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GAA |
MedGen: GAA (Human Medical Genetics with Condition) | |
ClinVar: GAA | |
Phenotype | MGI: GAA (International Mouse Phenotyping Consortium) |
PhenomicDB: GAA |
Mutations for GAA |
* 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 |
There's no inter-chromosomal structural variation. |
- 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 | GAA | chr17 | 78083258 | 78083278 | CCDC40 | chr17 | 78071945 | 78071965 |
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 GAA 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 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 2 |   |   | 1 | 3 |   |   |   |   |   | 1 |   |   | 1 |   |   |   | |||
GAIN (# sample) | 2 |   |   | 1 |   |   |   |   |   |   | 1 |   |   | 1 |   |   |   | |||
LOSS (# sample) |   |   |   |   | 3 |   |   |   |   |   |   |   |   |   |   |   |   |
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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=57) | (# total SNVs=32) |
(# total SNVs=3) | (# total SNVs=2) |
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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 |
chr17:78081655-78081655 | p.G305G | 4 |
chr17:78091405-78091405 | p.V780I | 4 |
chr17:78079669-78079669 | p.R223H | 3 |
chr17:78087109-78087109 | p.T711T | 3 |
chr17:78078709-78078709 | p.C108C | 3 |
chr17:78090819-78090819 | p.E748Q | 3 |
chr17:78081640-78081640 | p.A300A | 2 |
chr17:78091999-78091999 | p.G830V | 2 |
chr17:78078636-78078637 | p.N87fs*9 | 2 |
chr17:78081661-78081661 | p.A307A | 2 |
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SNV Counts per Each Loci in TCGA data |
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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 |   | 9 | 3 |   | 3 |   | 2 |   |   | 4 | 1 | 1 | 1 | 1 | 9 | 5 | 1 | 7 |
# mutation |   | 2 |   | 10 | 3 |   | 3 |   | 2 |   |   | 4 | 1 | 1 | 1 | 1 | 12 | 5 | 1 | 7 |
nonsynonymous SNV |   | 2 |   | 9 | 1 |   | 3 |   | 1 |   |   | 4 |   | 1 |   | 1 | 5 | 2 |   | 4 |
synonymous SNV |   |   |   | 1 | 2 |   |   |   | 1 |   |   |   | 1 |   | 1 |   | 7 | 3 | 1 | 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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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 |
chr17:78091451 | p.E795G,GAA | 2 |
chr17:78083851 | p.F245F,GAA | 1 |
chr17:78092558 | p.E521K,GAA | 1 |
chr17:78078786 | p.T777M,GAA | 1 |
chr17:78086728 | p.A261A,GAA | 1 |
chr17:78081639 | p.F525F,GAA | 1 |
chr17:78084546 | p.V778M,GAA | 1 |
chr17:78078846 | p.A300V,GAA | 1 |
chr17:78087028 | p.A554V,GAA | 1 |
chr17:78081640 | p.F35V,GAA | 1 |
Other DBs for Point Mutations |
Copy Number for GAA 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 GAA |
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)) |
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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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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 |
ANAPC11,ARHGDIA,ASPSCR1,OGFOD3,C17orf62,C17orf70,OXLD1, CHMP6,GAA,GPS1,GRN,HGS,LRPAP1,MAN1B1, MRPL12,NAGLU,P4HB,RFNG,SDF4,SGSH,SLC38A10 | ADAP1,AMDHD2,ABHD16A,MFSD12,CAPN1,CLCN7,CLN6, CNPY3,COMMD5,CORO1B,CYBA,DDX41,GAA,GHDC, GSDMD,MGAT4B,PNPLA6,TADA3,TMED9,UNC93B1,VPS18 | ||||
APOBEC3F,CHST12,GAA,GPSM1,GRN,HOMER3,PALM, PKN1,PLBD2,PLD3,PPM1K,PPP1R9B,PSAP,RNF144B, SCPEP1,SLC26A11,TTC7B,TTYH2,VAT1,XYLT2,ZNF385A | AKAP8L,ATP2C2,COX19,DPH1,EML3,FGFRL1,GAA, GAS6,HPS4,IFT122,IFT140,ING5,CCDC183,LINC00174, RIN1,SNAPC4,TOP1MT,TSC2,NELFA,ZNF446,ZNF497 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for GAA |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00284 | glucosidase, alpha; acid | approved; investigational | Acarbose | ||
DB00491 | glucosidase, alpha; acid | approved | Miglitol |
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Cross referenced IDs for GAA |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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