Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for GLUD1
Basic gene info.Gene symbolGLUD1
Gene nameglutamate dehydrogenase 1
SynonymsGDH|GDH1|GLUD
CytomapUCSC genome browser: 10q23.3
Genomic locationchr10 :88809958-88854776
Type of geneprotein-coding
RefGenesNM_005271.3,
Ensembl idENSG00000148672
DescriptionGDH 1glutamate dehydrogenase (NAD(P)+)glutamate dehydrogenase 1, mitochondrial
Modification date20141219
dbXrefs MIM : 138130
HGNC : HGNC
Ensembl : ENSG00000148672
HPRD : 11748
Vega : OTTHUMG00000018666
ProteinUniProt: P00367
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GLUD1
BioGPS: 2746
Gene Expression Atlas: ENSG00000148672
The Human Protein Atlas: ENSG00000148672
PathwayNCI Pathway Interaction Database: GLUD1
KEGG: GLUD1
REACTOME: GLUD1
ConsensusPathDB
Pathway Commons: GLUD1
MetabolismMetaCyc: GLUD1
HUMANCyc: GLUD1
RegulationEnsembl's Regulation: ENSG00000148672
miRBase: chr10 :88,809,958-88,854,776
TargetScan: NM_005271
cisRED: ENSG00000148672
ContextiHOP: GLUD1
cancer metabolism search in PubMed: GLUD1
UCL Cancer Institute: GLUD1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GLUD1 in cancer cell metabolism1. Son J, Lyssiotis CA, Ying H, Wang X, Hua S, et al. (2013) Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway. Nature 496: 101-105. doi: 10.1038/nature12040. pmid: 3656466. go to article

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Phenotypic Information for GLUD1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GLUD1
Familial Cancer Database: GLUD1
* This gene is included in those cancer gene databases.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM
KEGG_ARGININE_AND_PROLINE_METABOLISM
KEGG_NITROGEN_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM 138130; gene.
606762; phenotype.
Orphanet 35878; Hyperinsulinism-hyperammonemia syndrome.
DiseaseKEGG Disease: GLUD1
MedGen: GLUD1 (Human Medical Genetics with Condition)
ClinVar: GLUD1
PhenotypeMGI: GLUD1 (International Mouse Phenotyping Consortium)
PhenomicDB: GLUD1

Mutations for GLUD1
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryGLUD1chr108883129788831317CNTN5chr119943395499433974
ovaryGLUD1chr108883130188831321GLUD1chr108884442488844444
ovaryGLUD1chr108883130388831323GLUD1chr108884442488844444
ovaryGLUD1chr108883205788832077CNTN5chr119942725599427275
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GLUD1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM807517GLUD119186108881123888811405HBG21792011153505745350596
BI054523UPF21170101207111712071176GLUD159141108881118988811305

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample12            1  
GAIN (# sample)1                
LOSS (# sample)12            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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=26)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr10:88811597-88811597p.L530V2
chr10:88811617-88811617p.R523H2
chr10:88827869-88827869p.R231Q2
chr10:88835729-88835729p.Y193C1
chr10:88811533-88811533p.N551S1
chr10:88818945-88818945p.T455I1
chr10:88854358-88854358p.V57L1
chr10:88820771-88820771p.L320L1
chr10:88835744-88835744p.I188S1
chr10:88811588-88811588p.D533Y1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 5  3 2  241  47 6
# mutation21 5  3 2  541  47 6
nonsynonymous SNV2  3  2 2  33   14 3
synonymous SNV 1 2  1    211  33 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr10:88827869p.R231Q2
chr10:88836378p.I380I1
chr10:88811578p.V161I1
chr10:88819941p.T536I1
chr10:88822464p.S333S1
chr10:88836409p.I150I1
chr10:88811610p.A525A1
chr10:88819949p.R516C1
chr10:88822513p.L320L1
chr10:88813110p.D126G1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for GLUD1 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 GLUD1

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

ACADSB,ZFAND4,C10orf32,ESR1,FAM35A,FAM35DP,FAM35BP,
FOXA1,GLUD1,GLUD2,HCAR1,MOAP1,NDFIP1,PLA2G12A,
PTGR2,RAB5B,SLC39A9,TAPT1,TBC1D12,TTC8,XBP1
BZW1,CAB39L,DAZAP2,GLUD1,HIATL1,LOC653566,MEAF6,
PIGK,RAB11A,REEP5,SEC22C,SELT,SEP15,SLC44A1,
SNX14,TMCO1,TMEM59,SARAF,TMEM9B,UNC50,YWHAQ

ASCC1,ATAD1,ATP5C1,CALM2,COX15,CWF19L1,FAM35A,
FAM35BP,GDI2,GHITM,GLRX3,GLUD1,GLUD2,GSTO1,
MARCH5,MRPL43,NDUFB8,PCGF5,PPA1,SMNDC1,VPS26A
AKR1C3,BPHL,TMEM256,CRYL1,DERA,ELMOD2,FAM35A,
FAM35BP,FAM3B,CMTR2,GLUD1,GLUD2,GRAMD1C,MAPK8,
NCOA4,PHYH,PPP1CC,RRAS2,SAR1B,SUCLG1,TMEM139
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for GLUD1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA28737; -.
Organism-specific databasesCTD 2746; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00142glutamate dehydrogenase 1approved; nutraceuticalL-Glutamic Acid
DB00157glutamate dehydrogenase 1approved; nutraceuticalNADH
DB00756glutamate dehydrogenase 1approvedHexachlorophene
DB01907glutamate dehydrogenase 1experimentalNicotinamide-Adenine-Dinucleotide
DB03431glutamate dehydrogenase 1experimentalAdenosine-5'-Diphosphate
DB04137glutamate dehydrogenase 1experimentalGuanosine-5'-Triphosphate
DB00130glutamate dehydrogenase 1approved; nutraceutical; investigationalL-Glutamine


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Cross referenced IDs for GLUD1
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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