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 MDH2
Basic gene info.Gene symbolMDH2
Gene namemalate dehydrogenase 2, NAD (mitochondrial)
SynonymsM-MDH|MDH|MGC:3559|MOR1
CytomapUCSC genome browser: 7cen-q22
Genomic locationchr7 :75677392-75695930
Type of geneprotein-coding
RefGenesNM_001282403.1,
NM_001282404.1,NM_005918.3,NR_104165.1,
Ensembl idENSG00000262847
Descriptionmalate dehydrogenase, mitochondrial
Modification date20141207
dbXrefs MIM : 154100
HGNC : HGNC
Ensembl : ENSG00000146701
HPRD : 01099
Vega : OTTHUMG00000023827
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MDH2
BioGPS: 4191
Gene Expression Atlas: ENSG00000262847
The Human Protein Atlas: ENSG00000262847
PathwayNCI Pathway Interaction Database: MDH2
KEGG: MDH2
REACTOME: MDH2
ConsensusPathDB
Pathway Commons: MDH2
MetabolismMetaCyc: MDH2
HUMANCyc: MDH2
RegulationEnsembl's Regulation: ENSG00000262847
miRBase: chr7 :75,677,392-75,695,930
TargetScan: NM_001282403
cisRED: ENSG00000262847
ContextiHOP: MDH2
cancer metabolism search in PubMed: MDH2
UCL Cancer Institute: MDH2
Assigned class in ccmGDBC

Top
Phenotypic Information for MDH2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MDH2
Familial Cancer Database: MDH2
* 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_PYRUVATE_METABOLISM
KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: MDH2
MedGen: MDH2 (Human Medical Genetics with Condition)
ClinVar: MDH2
PhenotypeMGI: MDH2 (International Mouse Phenotyping Consortium)
PhenomicDB: MDH2

Mutations for MDH2
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasMDH2chr77568924575689265STK3chr89962353799623557
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 MDH2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP259062MDH2123477567742475684260LOC100507412229448?109556109774
BF794536MDH22410277569560175695679MDH29134077569565875695908

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=9

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=35)
Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr7:75677504-75677504p.A9V9
chr7:75686766-75686766p.G92C2
chr7:75692906-75692906p.S210C2
chr7:75687331-75687331p.A122S2
chr7:75693664-75693664p.P214L2
chr7:75694234-75694234p.T283M2
chr7:75689759-75689759p.I166I1
chr7:75693701-75693701p.L226L1
chr7:75686754-75686754p.D88Y1
chr7:75694266-75694266p.L294F1

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
# sample 1 4  1    3221 81 5
# mutation 1 4  1    3221 81 5
nonsynonymous SNV 1 3       2121 41 3
synonymous SNV   1  1    11   4  2
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
chr7:75695601p.K255R,MDH22
chr7:75693708p.G34E,MDH21
chr7:75687295p.P177L,MDH21
chr7:75694157p.S51G,MDH21
chr7:75687336p.R187W,MDH21
chr7:75694217p.D57H,MDH21
chr7:75689711p.R215R,MDH21
chr7:75694218p.L81L,MDH21
chr7:75684173p.F235F,MDH21
chr7:75689759p.G92C,MDH21

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 MDH2 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 MDH2

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

AHSA1,AIMP2,AP1S1,ARPC1A,ATP5J2,BUD31,CPSF4,
EIF3B,MDH2,MRPL4,NSUN5,PDAP1,POLD2,POR,
RFC2,STYXL1,SUCLG1,TBRG4,TMEM120A,WBSCR16,WBSCR22
ADSL,ALDOA,ATP5A1,COQ9,CYC1,DYRK1B,GAMT,
GAPDH,MACROD1,MDH2,NDUFB10,NDUFS2,NDUFS3,POLDIP2,
RAD23A,RPUSD4,SLC25A11,TPI1,TRPT1,UBAC1,UQCRC1

AP1S1,ARPC1A,ASL,ATP5J2,CHCHD3,COPS6,CPSF4,
FIS1,GNB2,LRWD1,MDH2,MRPS24,NDUFB2,NSUN5,
PDAP1,POP7,PTCD1,RFC2,WBSCR16,WBSCR22,ZP3
ATP5A1,ATP5B,ATP5D,CHCHD10,COQ4,COX5A,ECHS1,
ETFB,FH,GLRX5,IDH3B,IDH3G,MDH2,MRPL23,
MTCH2,NDUFV1,SAMM50,TALDO1,TPI1,TUFM,UQCRC1
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 MDH2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00157malate dehydrogenase 2, NAD (mitochondrial)approved; nutraceuticalNADH
DB04272malate dehydrogenase 2, NAD (mitochondrial)experimentalCitric Acid
DB00121malate dehydrogenase 2, NAD (mitochondrial)approved; nutraceuticalBiotin


Top
Cross referenced IDs for MDH2
* 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