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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GLUD2 |
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Phenotypic Information for GLUD2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GLUD2 |
Familial Cancer Database: GLUD2 |
* 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_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM KEGG_ARGININE_AND_PROLINE_METABOLISM KEGG_NITROGEN_METABOLISM |
Others | |
OMIM | 300144; gene. |
Orphanet | |
Disease | KEGG Disease: GLUD2 |
MedGen: GLUD2 (Human Medical Genetics with Condition) | |
ClinVar: GLUD2 | |
Phenotype | MGI: GLUD2 (International Mouse Phenotyping Consortium) |
PhenomicDB: GLUD2 |
Mutations for GLUD2 |
* 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 GLUD2 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=79) | (# total SNVs=24) |
(# total SNVs=1) | (# 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 |
chr23:120181966-120181966 | p.R143H | 3 |
chr23:120183007-120183007 | p.T490M | 2 |
chr23:120182660-120182660 | p.V374V | 2 |
chr23:120183038-120183038 | p.A500A | 2 |
chr23:120183085-120183085 | p.R516H | 2 |
chr23:120181970-120181970 | p.T144T | 2 |
chr23:120182230-120182230 | p.R231Q | 2 |
chr23:120181778-120181778 | p.I80I | 2 |
chr23:120182035-120182035 | p.S166Y | 2 |
chr23:120182312-120182312 | p.K258K | 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 | 2 |   | 24 | 4 |   | 6 | 1 | 1 |   |   | 11 | 8 | 2 |   |   | 4 | 6 |   | 14 |
# mutation | 2 | 2 |   | 24 | 4 |   | 6 | 1 | 1 |   |   | 12 | 8 | 2 |   |   | 5 | 7 |   | 17 |
nonsynonymous SNV | 1 | 1 |   | 20 | 3 |   | 4 | 1 |   |   |   | 9 | 6 | 2 |   |   | 2 | 6 |   | 12 |
synonymous SNV | 1 | 1 |   | 4 | 1 |   | 2 |   | 1 |   |   | 3 | 2 |   |   |   | 3 | 1 |   | 5 |
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 |
chrX:120182230 | p.R231Q | 3 |
chrX:120181778 | p.V374V | 2 |
chrX:120182660 | p.T144T | 2 |
chrX:120181970 | p.I80I | 2 |
chrX:120182613 | p.R268H | 1 |
chrX:120181909 | p.E368V | 1 |
chrX:120182071 | p.A432P | 1 |
chrX:120182730 | p.F66L | 1 |
chrX:120181654 | p.S128P | 1 |
chrX:120182430 | p.G294R | 1 |
Other DBs for Point Mutations |
Copy Number for GLUD2 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 GLUD2 |
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 |
ACADSB,ALDH6A1,ATG2B,DMXL1,FAM35A,FNIP1,GIGYF2, GLUD1,GLUD2,GMCL1,HCAR1,IDE,LCOR,LRBA, MARCH8,NHLRC2,PCYOX1,RAPGEF6,RASEF,TBC1D12,WAPAL | AR,ATF2,COPA,EPB41L5,GLUD2,NOTCH2,OCRL, OPHN1,PAFAH1B2,PTPN13,RAB3GAP1,RHBDD1,RSRC1,SCARB2, SEL1L,SLC30A6,TRIM44,UEVLD,UTP14C,WWC2,YIPF6 | ||||
ATAD1,CHUK,CRK,DDX21,ERLIN1,FAM35A,FAM35DP, FAM35BP,FAM45B,GLUD1,GLUD2,HNRNPLL,HSPA8,IDE, LOC284441,MAPK8,NCOA4,PAFAH1B2,PGAM4,TCTN3,WBP11P1 | AKR1B15,BPHL,CRYL1,ELMOD2,FAM35A,FAM35DP,FAM35BP, FASTKD3,CMTR2,GLUD1,GLUD2,HADH,MAPK8,NCOA4, PPP1CC,SAR1B,SDHB,SLC14A2,SLC25A16,SUCLG1,TBC1D15 |
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 GLUD2 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Organism-specific databases | PharmGKB | PA28738; -. |
Organism-specific databases | CTD | 2747; -. |
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 |
DB00142 | glutamate dehydrogenase 2 | approved; nutraceutical | L-Glutamic Acid | ||
DB00157 | glutamate dehydrogenase 2 | approved; nutraceutical | NADH | ||
DB01907 | glutamate dehydrogenase 2 | experimental | Nicotinamide-Adenine-Dinucleotide |
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Cross referenced IDs for GLUD2 |
* 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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