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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GPAA1 |
Basic gene info. | Gene symbol | GPAA1 |
Gene name | glycosylphosphatidylinositol anchor attachment 1 | |
Synonyms | GAA1|hGAA1 | |
Cytomap | UCSC genome browser: 8q24.3 | |
Genomic location | chr8 :145137523-145141119 | |
Type of gene | protein-coding | |
RefGenes | NM_003801.3, | |
Ensembl id | ENSG00000260226 | |
Description | GAA1 protein homologGPAA1P anchor attachment protein 1 homologGPI anchor attachment protein 1GPI transamidase subunitanchor attachment protein 1 (Gaa1p, yeast) homologglycophosphatidylinositol anchor attachment 1glycosylphosphatidylinositol anchor a | |
Modification date | 20141207 | |
dbXrefs | MIM : 603048 | |
HGNC : HGNC | ||
Ensembl : ENSG00000197858 | ||
HPRD : 04334 | ||
Vega : OTTHUMG00000165438 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GPAA1 | |
BioGPS: 8733 | ||
Gene Expression Atlas: ENSG00000260226 | ||
The Human Protein Atlas: ENSG00000260226 | ||
Pathway | NCI Pathway Interaction Database: GPAA1 | |
KEGG: GPAA1 | ||
REACTOME: GPAA1 | ||
ConsensusPathDB | ||
Pathway Commons: GPAA1 | ||
Metabolism | MetaCyc: GPAA1 | |
HUMANCyc: GPAA1 | ||
Regulation | Ensembl's Regulation: ENSG00000260226 | |
miRBase: chr8 :145,137,523-145,141,119 | ||
TargetScan: NM_003801 | ||
cisRED: ENSG00000260226 | ||
Context | iHOP: GPAA1 | |
cancer metabolism search in PubMed: GPAA1 | ||
UCL Cancer Institute: GPAA1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for GPAA1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GPAA1 |
Familial Cancer Database: GPAA1 |
* This gene is included in those cancer gene databases. |
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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 | |
REACTOME_METABOLISM_OF_PROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GPAA1 |
MedGen: GPAA1 (Human Medical Genetics with Condition) | |
ClinVar: GPAA1 | |
Phenotype | MGI: GPAA1 (International Mouse Phenotyping Consortium) |
PhenomicDB: GPAA1 |
Mutations for GPAA1 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GPAA1 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 |
There's no copy number variation information in COSMIC data for this gene. |
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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=29) | (# total SNVs=13) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr8:145139397-145139397 | p.S299P | 4 |
chr8:145139412-145139412 | p.G304S | 2 |
chr8:145139460-145139460 | p.R320C | 2 |
chr8:145139522-145139522 | p.? | 2 |
chr8:145139669-145139669 | p.R352L | 2 |
chr8:145140316-145140316 | p.E462G | 2 |
chr8:145140382-145140382 | p.R484Q | 2 |
chr8:145139400-145139400 | p.G300S | 2 |
chr8:145139129-145139129 | p.V237L | 1 |
chr8:145140621-145140621 | p.A533S | 1 |
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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 | 1 | 1 |   | 7 |   |   | 3 | 1 | 1 |   |   | 5 | 5 |   |   |   | 2 | 7 |   | 2 |
# mutation | 1 | 1 |   | 7 |   |   | 3 | 1 | 1 |   |   | 5 | 5 |   |   |   | 2 | 8 |   | 3 |
nonsynonymous SNV | 1 | 1 |   | 5 |   |   | 1 | 1 | 1 |   |   | 2 | 3 |   |   |   |   | 5 |   | 3 |
synonymous SNV |   |   |   | 2 |   |   | 2 |   |   |   |   | 3 | 2 |   |   |   | 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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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 |
chr8:145139460 | p.G300S | 2 |
chr8:145139718 | p.R320C | 2 |
chr8:145139400 | p.F368F | 2 |
chr8:145140516 | p.G191V | 1 |
chr8:145138862 | p.S426S | 1 |
chr8:145139491 | p.F255F | 1 |
chr8:145140569 | p.L431L | 1 |
chr8:145138897 | p.C259F | 1 |
chr8:145139713 | p.G448G | 1 |
chr8:145140621 | p.T267T | 1 |
Other DBs for Point Mutations |
Copy Number for GPAA1 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 GPAA1 |
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 |
ADCK5,HGH1,COMMD5,CYC1,CYHR1,DGAT1,EXOSC4, FBXL6,GPAA1,SLC52A2,HSF1,LRRC14,MAF1,MFSD3, PPP1R16A,PUF60,PYCRL,SCRIB,SHARPIN,TIGD5,VPS28 | C19orf24,C9orf16,COPE,GPAA1,GPR137,SLC52A2,GUK1, JMJD8,MOSPD3,MRPS12,NUBP2,NUDT22,PPP1CA,PPP4C, SLC25A39,SSSCA1,TMEM222,YIF1B,ZDHHC12,ZDHHC24,ZFPL1 |
HGH1,CHRAC1,COMMD5,CYC1,CYHR1,EEF1D,EXOSC4, GPAA1,HSF1,LRRC14,MAF1,MFSD3,PPP1R16A,PUF60, PYCRL,RECQL4,SCRIB,SHARPIN,TIGD5,VPS28,ZC3H3 | ATP5D,ELMO3,EPN1,ESRRA,ETFB,FBXW5,GPAA1, ILVBL,MAP3K11,MGAT4B,NAGPA,NAPRT,NBL1,PEX16, PPP1R16A,RILP,SDF4,SLC25A1,TMUB1,TNIP2,ZDHHC12 |
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 GPAA1 |
There's no related Drug. |
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Cross referenced IDs for GPAA1 |
* 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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