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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GBE1 |
Basic gene info. | Gene symbol | GBE1 |
Gene name | glucan (1,4-alpha-), branching enzyme 1 | |
Synonyms | APBD|GBE|GSD4 | |
Cytomap | UCSC genome browser: 3p12.3 | |
Genomic location | chr3 :81538849-81810950 | |
Type of gene | protein-coding | |
RefGenes | NM_000158.3, | |
Ensembl id | ENSG00000114480 | |
Description | 1,4-alpha-glucan-branching enzymeamylo-(1,4 to 1,6) transglucosidaseamylo-(1,4 to 1,6) transglycosylasebrancher enzymeglycogen branching enzymeglycogen-branching enzyme | |
Modification date | 20141219 | |
dbXrefs | MIM : 607839 | |
HGNC : HGNC | ||
Ensembl : ENSG00000114480 | ||
HPRD : 01985 | ||
Vega : OTTHUMG00000158978 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GBE1 | |
BioGPS: 2632 | ||
Gene Expression Atlas: ENSG00000114480 | ||
The Human Protein Atlas: ENSG00000114480 | ||
Pathway | NCI Pathway Interaction Database: GBE1 | |
KEGG: GBE1 | ||
REACTOME: GBE1 | ||
ConsensusPathDB | ||
Pathway Commons: GBE1 | ||
Metabolism | MetaCyc: GBE1 | |
HUMANCyc: GBE1 | ||
Regulation | Ensembl's Regulation: ENSG00000114480 | |
miRBase: chr3 :81,538,849-81,810,950 | ||
TargetScan: NM_000158 | ||
cisRED: ENSG00000114480 | ||
Context | iHOP: GBE1 | |
cancer metabolism search in PubMed: GBE1 | ||
UCL Cancer Institute: GBE1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for GBE1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GBE1 |
Familial Cancer Database: GBE1 |
* 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 | |
KEGG_STARCH_AND_SUCROSE_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GBE1 |
MedGen: GBE1 (Human Medical Genetics with Condition) | |
ClinVar: GBE1 | |
Phenotype | MGI: GBE1 (International Mouse Phenotyping Consortium) |
PhenomicDB: GBE1 |
Mutations for GBE1 |
* 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 | GBE1 | chr3 | 81764439 | 81764459 | GBE1 | chr3 | 81711609 | 81711629 |
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 GBE1 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 |
BF346361 | PLCB4 | 582 | 621 | 20 | 9149571 | 9149611 | GBE1 | 621 | 648 | 3 | 81780156 | 81780186 | |
CA428629 | GBE1 | 2 | 120 | 3 | 81562616 | 81562736 | ITGA3 | 118 | 556 | 17 | 48145617 | 48149439 |
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 | 1 | 1 | 1 |   |   |   |   |   |   |   | 2 |   |   | 2 |   |   |   | |||
GAIN (# sample) | 1 |   |   |   |   |   |   |   |   |   | 1 |   |   | 2 |   |   |   | |||
LOSS (# sample) |   | 1 | 1 |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |
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=52) | (# total SNVs=20) |
(# total SNVs=2) | (# 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 |
chr3:81643118-81643118 | p.R350H | 3 |
chr3:81754677-81754677 | p.G77G | 3 |
chr3:81695576-81695576 | p.G250A | 2 |
chr3:81586104-81586104 | p.M587I | 2 |
chr3:81754702-81754702 | p.F69C | 2 |
chr3:81640303-81640303 | p.S374* | 2 |
chr3:81699052-81699052 | p.S150S | 2 |
chr3:81695559-81695559 | p.F256V | 1 |
chr3:81754708-81754708 | p.D67V | 1 |
chr3:81586234-81586234 | p.G544E | 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 | 2 | 4 |   | 13 |   |   |   |   | 1 |   |   | 2 | 2 | 2 |   | 1 | 9 | 4 | 1 | 13 |
# mutation | 1 | 4 |   | 12 |   |   |   |   | 1 |   |   | 2 | 2 | 2 |   | 1 | 9 | 4 | 1 | 14 |
nonsynonymous SNV | 1 | 3 |   | 9 |   |   |   |   | 1 |   |   | 2 | 2 |   |   | 1 | 9 | 4 |   | 10 |
synonymous SNV |   | 1 |   | 3 |   |   |   |   |   |   |   |   |   | 2 |   |   |   |   | 1 | 4 |
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 |
chr3:81586104 | p.S150S | 2 |
chr3:81699052 | p.R350H | 2 |
chr3:81640218 | p.T402T | 2 |
chr3:81643118 | p.M587I | 2 |
chr3:81754734 | p.L363F | 1 |
chr3:81630387 | p.D571D | 1 |
chr3:81691953 | p.L142F | 1 |
chr3:81699046 | p.R565W | 1 |
chr3:81584455 | p.R336K | 1 |
chr3:81810599 | p.K115N | 1 |
Other DBs for Point Mutations |
Copy Number for GBE1 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 GBE1 |
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 |
ANO6,ATP6V1A,EOGT,CCNYL1,CD109,CHMP2B,CSGALNACT2, ERO1L,FERMT2,FNDC3B,FUT11,GBE1,ITGAV,ITGB1, KIAA1715,LIMS1,LOX,NCKAP1,P4HA1,PTPLB,ZNF654 | ACAA2,ACO1,ACSS2,BNIP3,PQLC2L,CIDEC,FAM89A, GBE1,GYG2,HSDL2,MARC1,MTHFD1,PEX19,PFKFB1, PPARG,PPP1R1A,PRDX6,PRKAR2B,RNF157,STBD1,TSPAN3 | ||||
BNIP3L,TMEM263,C4orf3,CA9,ERO1L,FUT11,GBE1, HIF1A,LDHA,MAPK6,P4HA1,PDK1,PFKFB3,PGAM1, PLOD2,SEC24D,SSR3,STC1,TMEM45A,TMTC3,ZNF654 | ANXA2P1,CAND1,DLD,EPB41L2,FBXL17,GBE1,HNRNPK, HSPA4,IDE,INTS4P1,KIAA1279,NARS,PAK2,PARG, PPP3R1,PSMD1,RAB14,RDH8,UBE3A,UBP1,YME1L1 |
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 GBE1 |
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 |
DB01033 | glucan (1,4-alpha-), branching enzyme 1 | approved | Mercaptopurine | ||
DB00563 | glucan (1,4-alpha-), branching enzyme 1 | approved | Methotrexate |
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Cross referenced IDs for GBE1 |
* 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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