|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GBA |
Top |
Phenotypic Information for GBA(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GBA |
Familial Cancer Database: GBA |
* 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_SPHINGOLIPID_METABOLISM REACTOME_GLYCOSPHINGOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GBA |
MedGen: GBA (Human Medical Genetics with Condition) | |
ClinVar: GBA | |
Phenotype | MGI: GBA (International Mouse Phenotyping Consortium) |
PhenomicDB: GBA |
Mutations for GBA |
* 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 GBA 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 |
Top |
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 |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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) |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=29) | (# total SNVs=14) |
(# total SNVs=1) | (# total SNVs=0) |
Top |
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 |
chr1:155206068-155206068 | p.R398* | 5 |
chr1:155208097-155208097 | p.I197V | 2 |
chr1:155210491-155210491 | p.L15F | 2 |
chr1:155207160-155207160 | p.R324H | 1 |
chr1:155209482-155209482 | p.A127T | 1 |
chr1:155207291-155207291 | p.L280F | 1 |
chr1:155209863-155209863 | p.R41C | 1 |
chr1:155205593-155205593 | p.A423S | 1 |
chr1:155208037-155208037 | p.P217S | 1 |
chr1:155207162-155207162 | p.Q323Q | 1 |
Top |
SNV Counts per Each Loci in TCGA data |
|
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 | 1 |   | 6 |   |   | 2 |   | 4 |   |   | 9 | 5 | 1 |   |   | 2 | 5 |   | 6 |
# mutation | 3 | 1 |   | 6 |   |   | 2 |   | 4 |   |   | 9 | 5 | 1 |   |   | 3 | 6 |   | 6 |
nonsynonymous SNV | 2 | 1 |   | 3 |   |   | 2 |   | 2 |   |   | 4 | 4 |   |   |   | 3 | 5 |   | 4 |
synonymous SNV | 1 |   |   | 3 |   |   |   |   | 2 |   |   | 5 | 1 | 1 |   |   |   | 1 |   | 2 |
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]) |
Top |
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 |
chr1:155207267 | p.Q236Q,GBA | 1 |
chr1:155208008 | p.A142A,GBA | 1 |
chr1:155206085 | p.L25L,GBA | 1 |
chr1:155209779 | p.Q236R,GBA | 1 |
chr1:155207269 | p.T139T,GBA | 1 |
chr1:155208036 | p.R17M,GBA | 1 |
chr1:155206139 | p.D235N,GBA | 1 |
chr1:155209863 | p.P130H,GBA | 1 |
chr1:155207291 | p.R229C,GBA | 1 |
chr1:155208037 | p.P130S,GBA | 1 |
Other DBs for Point Mutations |
Copy Number for GBA 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] |
Top |
Gene Expression for GBA |
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)) |
Top |
CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
Top |
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 |
ADAM18,BAGE,C11orf53,NAT16,CLCA1,CT47A11,DDC, FLJ25363,GBA3,HAND1,HTR2C,KCNA4,KCNK12,KRTAP9-4, KRTAP9-9,LOC360030,POU4F2,RLN3,SEC14L3,SHH,SPANXA2 | CDKN2AIP,GBA3,GUCA1C,KANSL1,KRTAP12-2,CERS3,MAP3K1, MMS19,STK26,NKX6-2,OR4A47,OR52B2,OR6S1,OVCH2, PARP16,PTPRZ1,SCN2A,SNHG1,TMCO6,WIF1,ZNF354A | ||||
AMPD1,ADTRP,CA2,CASR,CDKN2B-AS1,CYP2C18,DRD5, DUSP21,ENPP6,GBA3,GPT,GUCA2B,HSD3B2,MEP1B, MS4A12,NR1H4,OTOP2,SLC17A8,SLC25A34,SLC30A10,TMIGD1 | ACE2,ANPEP,ADIRF,CHN2,FLVCR1,G6PC,GBA3, SLC52A1,HEBP1,MEP1B,MS4A8,NAT8B,OTC,PCK2, PEPD,PKLR,PTGR1,SLC17A8,SLC23A1,SLC6A4,AGMO |
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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for GBA |
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 |
DB03106 | glucosidase, beta, acid | experimental | Myo-Inositol | ||
DB03740 | glucosidase, beta, acid | experimental | 2-(Acetylamino)-2-Deoxy-a-D-Glucopyranose | ||
DB08283 | glucosidase, beta, acid | experimental | (2R,3R,4R,5S)-2-(HYDROXYMETHYL)-1-NONYLPIPERIDINE-3,4,5-TRIOL |
Top |
Cross referenced IDs for GBA |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |