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 D2HGDH
Basic gene info.Gene symbolD2HGDH
Gene nameD-2-hydroxyglutarate dehydrogenase
SynonymsD2HGD
CytomapUCSC genome browser: 2q37.3
Genomic locationchr2 :242674029-242708231
Type of geneprotein-coding
RefGenesNM_001287249.1,
NM_152783.4,NR_109778.1,
Ensembl idENSG00000180902
DescriptionD-2-hydroxyglutarate dehydrogenase, mitochondrial
Modification date20141207
dbXrefs MIM : 609186
HGNC : HGNC
Ensembl : ENSG00000180902
HPRD : 14502
Vega : OTTHUMG00000151474
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_D2HGDH
BioGPS: 728294
Gene Expression Atlas: ENSG00000180902
The Human Protein Atlas: ENSG00000180902
PathwayNCI Pathway Interaction Database: D2HGDH
KEGG: D2HGDH
REACTOME: D2HGDH
ConsensusPathDB
Pathway Commons: D2HGDH
MetabolismMetaCyc: D2HGDH
HUMANCyc: D2HGDH
RegulationEnsembl's Regulation: ENSG00000180902
miRBase: chr2 :242,674,029-242,708,231
TargetScan: NM_001287249
cisRED: ENSG00000180902
ContextiHOP: D2HGDH
cancer metabolism search in PubMed: D2HGDH
UCL Cancer Institute: D2HGDH
Assigned class in ccmGDBC

Top
Phenotypic Information for D2HGDH(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: D2HGDH
Familial Cancer Database: D2HGDH
* 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
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: D2HGDH
MedGen: D2HGDH (Human Medical Genetics with Condition)
ClinVar: D2HGDH
PhenotypeMGI: D2HGDH (International Mouse Phenotyping Consortium)
PhenomicDB: D2HGDH

Mutations for D2HGDH
* 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 D2HGDH related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF920776D2HGDH333312242690672242695430HDGFRP23283481945002244500244

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample          1      
GAIN (# sample)          1      
LOSS (# sample)                 
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)

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=5

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=40)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr2:242674803-242674803p.R55Q5
chr2:242681891-242681891p.G131V2
chr2:242689687-242689687p.L325L2
chr2:242695381-242695381p.A420T2
chr2:242681845-242681845p.?1
chr2:242690737-242690737p.L358L1
chr2:242683123-242683123p.G193R1
chr2:242695407-242695407p.H428H1
chr2:242674768-242674768p.P43P1
chr2:242684288-242684288p.F283F1

Top
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
# sample12 13   2  62   4419
# mutation12 13   2  62   4419
nonsynonymous SNV11 12   1  31   24 5
synonymous SNV 1  1   1  31   2 14
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
chr2:242695381p.A286T,D2HGDH2
chr2:242683055p.T80T1
chr2:242690737p.T127T,D2HGDH1
chr2:242674879p.E313K,D2HGDH1
chr2:242707157p.V102M1
chr2:242683078p.F149F,D2HGDH1
chr2:242690743p.G343A,D2HGDH1
chr2:242680459p.P106P1
chr2:242707248p.E177E,D2HGDH1
chr2:242683123p.L371L,D2HGDH1

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 D2HGDH 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 D2HGDH

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

ANKS3,LMNTD2,CAPN10,D2HGDH,CRACR2B,EGFL8,FAM193B,
IDUA,JMJD7-PLA2G4B,LOC338799,PIDD1,NOXA1,PCSK4,RHOT2,
CLASRP,SNRNP70,SPSB3,TELO2,UBXN11,WASH7P,ZNF692
ANAPC2,CCDC130,CENPT,CPSF3L,D2HGDH,GGA1,GIGYF1,
HEXDC,HSF4,PIDD1,MUS81,NEURL4,OBSL1,OGFOD2,
RHOT2,SH2B1,SNRNP70,SYMPK,TOP3B,TRMT1,TRMT2A

AGAP4,AHSA2,ANKMY1,ATG4B,CCNL2,CDK10,CYP2D7,
D2HGDH,ECHDC2,HSF4,ING5,JMJD7-PLA2G4B,LOC100130015,MSH5,
NSUN5P1,NSUN5P2,PILRB,TAF1C,ZNF276,ZNF692,ZNF767P
ADAMTS13,ADCY6,ARHGAP39,ARHGEF10L,ATG16L2,CAPN3,D2HGDH,
DDX26B,DLL1,ENGASE,ESRP2,HDAC6,ING5,MSH5,
PLEKHH1,REXO1,SH2B1,TFCP2L1,TLN2,TRIM41,ZNF276
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 D2HGDH


There's no related Drug.
Top
Cross referenced IDs for D2HGDH
* 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