Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 GLUD2
Basic gene info.Gene symbolGLUD2
Gene nameglutamate dehydrogenase 2
SynonymsGDH2|GLUDP1
CytomapUCSC genome browser: Xq24-q25
Genomic locationchrX :120181461-120183796
Type of geneprotein-coding
RefGenesNM_012084.3,
Ensembl idENSG00000182890
DescriptionGDH 2glutamate dehydrogenase 2, mitochondrialglutamate dehydrogenase pseudogene 1
Modification date20141207
dbXrefs MIM : 300144
HGNC : HGNC
Ensembl : ENSG00000182890
HPRD : 02143
Vega : OTTHUMG00000022320
ProteinUniProt: P49448
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GLUD2
BioGPS: 2747
Gene Expression Atlas: ENSG00000182890
The Human Protein Atlas: ENSG00000182890
PathwayNCI Pathway Interaction Database: GLUD2
KEGG: GLUD2
REACTOME: GLUD2
ConsensusPathDB
Pathway Commons: GLUD2
MetabolismMetaCyc: GLUD2
HUMANCyc: GLUD2
RegulationEnsembl's Regulation: ENSG00000182890
miRBase: chrX :120,181,461-120,183,796
TargetScan: NM_012084
cisRED: ENSG00000182890
ContextiHOP: GLUD2
cancer metabolism search in PubMed: GLUD2
UCL Cancer Institute: GLUD2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

Top
Phenotypic Information for GLUD2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GLUD2
Familial Cancer Database: GLUD2
* 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

check002.gifOthers
OMIM 300144; gene.
Orphanet
DiseaseKEGG Disease: GLUD2
MedGen: GLUD2 (Human Medical Genetics with Condition)
ClinVar: GLUD2
PhenotypeMGI: 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GLUD2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

Top
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=4

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=79)
Stat. for Synonymous SNVs
(# total SNVs=24)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
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
chr23:120181966-120181966p.R143H3
chr23:120182035-120182035p.S166Y2
chr23:120182312-120182312p.K258K2
chr23:120183007-120183007p.T490M2
chr23:120182660-120182660p.V374V2
chr23:120183038-120183038p.A500A2
chr23:120183085-120183085p.R516H2
chr23:120181970-120181970p.T144T2
chr23:120181778-120181778p.I80I2
chr23:120182230-120182230p.R231Q2

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22 244 611  1182  46 14
# mutation22 244 611  1282  57 17
nonsynonymous SNV11 203 41   962  26 12
synonymous SNV11 41 2 1  32   31 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])

Top
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
chrX:120182230p.R231Q3
chrX:120182660p.V374V2
chrX:120181970p.I80I2
chrX:120181778p.T144T2
chrX:120181692p.E61K1
chrX:120182771p.R124H1
chrX:120181790p.A241T1
chrX:120182522p.L359L1
chrX:120183085p.I422I1
chrX:120181925p.D63N1

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 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]

Top
Gene Expression for GLUD2

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

: Open all plots for all cancer types


Top
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,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
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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for GLUD2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA28738; -.
Organism-specific databasesCTD 2747; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00142glutamate dehydrogenase 2approved; nutraceuticalL-Glutamic Acid
DB00157glutamate dehydrogenase 2approved; nutraceuticalNADH
DB01907glutamate dehydrogenase 2experimentalNicotinamide-Adenine-Dinucleotide


Top
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

: Open all cross reference information



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas