Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 DMGDH
Basic gene info.Gene symbolDMGDH
Gene namedimethylglycine dehydrogenase
SynonymsDMGDHD|ME2GLYDH
CytomapUCSC genome browser: 5q14.1
Genomic locationchr5 :78293428-78365449
Type of geneprotein-coding
RefGenesNM_013391.3,
NR_104002.1,NR_104003.1,
Ensembl idENSG00000132837
Descriptiondimethylglycine dehydrogenase, mitochondrial
Modification date20141211
dbXrefs MIM : 605849
HGNC : HGNC
Ensembl : ENSG00000132837
HPRD : 05789
Vega : OTTHUMG00000108159
ProteinUniProt: Q9UI17
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DMGDH
BioGPS: 29958
Gene Expression Atlas: ENSG00000132837
The Human Protein Atlas: ENSG00000132837
PathwayNCI Pathway Interaction Database: DMGDH
KEGG: DMGDH
REACTOME: DMGDH
ConsensusPathDB
Pathway Commons: DMGDH
MetabolismMetaCyc: DMGDH
HUMANCyc: DMGDH
RegulationEnsembl's Regulation: ENSG00000132837
miRBase: chr5 :78,293,428-78,365,449
TargetScan: NM_013391
cisRED: ENSG00000132837
ContextiHOP: DMGDH
cancer metabolism search in PubMed: DMGDH
UCL Cancer Institute: DMGDH
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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

check002.gifOthers
OMIM 605849; gene.
605850; phenotype.
Orphanet 243343; Dimethylglycine dehydrogenase deficiency.
DiseaseKEGG Disease: DMGDH
MedGen: DMGDH (Human Medical Genetics with Condition)
ClinVar: DMGDH
PhenotypeMGI: DMGDH (International Mouse Phenotyping Consortium)
PhenomicDB: DMGDH

Mutations for DMGDH
* 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 DMGDH 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

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample      2          
GAIN (# sample)                 
LOSS (# sample)      2          
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=66)
Stat. for Synonymous SNVs
(# total SNVs=23)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=0)
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
chr5:78340231-78340231p.S297L4
chr5:78326677-78326677p.L554L2
chr5:78322314-78322314p.D708G2
chr5:78325734-78325734p.D603N2
chr5:78338173-78338173p.P376S2
chr5:78340364-78340364p.R253C2
chr5:78340375-78340375p.G249E2
chr5:78359429-78359429p.?2
chr5:78340240-78340240p.L294Q2
chr5:78320134-78320134p.P737H2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13 152 1 4  532  141017
# mutation13 172 2 4  732  161017
nonsynonymous SNV 3 112 1 3  532  10714
synonymous SNV1  6  1 1  2    63 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
chr5:78322314p.D696D2
chr5:78338268p.S276L2
chr5:78322349p.R253C2
chr5:78326677p.P376S2
chr5:78340294p.D708G2
chr5:78338173p.R344Q2
chr5:78340364p.L554L2
chr5:78350168p.R153R1
chr5:78328527p.M699R1
chr5:78324471p.S520P1

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 DMGDH 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 DMGDH

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

ABCA6,ABCA8,ABCA9,ANGPTL1,AOC3,ARHGAP20,BHMT2,
CCDC80,DMGDH,GGNBP1,IGF1,LAMA2,LDB2,LHFP,
NKAPL,PDE2A,PLSCR4,SCN7A,SH3D19,TNS1,VWF
ACO1,AOC3,CLMP,ASPH,MTURN,CAT,DMGDH,
EHBP1,FERMT2,HRASLS5,LAMA4,MMD,MRAS,PALM2-AKAP2,
PLIN1,PYGL,SLC25A16,SORBS1,TNS1,TSPAN3,VKORC1L1

ABCA8,ABCA9,ADH1B,AQPEP,ART4,BHMT2,CYP11A1,
DMGDH,LEPR,LOC339524,NIPSNAP3B,PCDHGA2,PLIN4,POLN,
RBP7,SEMA3G,TAS2R41,TMEM178A,TMEM91,UPK1A,ZNF382
AGTR1,ANGPTL1,ARMCX1,DDIT4L,DIXDC1,DMGDH,DZIP1,
GLRB,HLF,HRASLS5,LOC285548,NKX3-2,NNAT,NOX4,
PGM5,RGS4,RHOJ,SCD5,SOX15,SSBP2,TMEM35
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 DMGDH


There's no related Drug.
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Cross referenced IDs for DMGDH
* 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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