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 MDH1
Basic gene info.Gene symbolMDH1
Gene namemalate dehydrogenase 1, NAD (soluble)
SynonymsHEL-S-32|MDH-s|MDHA|MGC:1375|MOR2
CytomapUCSC genome browser: 2p13.3
Genomic locationchr2 :63816284-63834330
Type of geneprotein-coding
RefGenesNM_001199111.1,
NM_001199112.1,NM_005917.3,
Ensembl idENSG00000014641
Descriptioncytosolic malate dehydrogenasediiodophenylpyruvate reductaseepididymis secretory protein Li 32malate dehydrogenase, cytoplasmicsoluble malate dehydrogenase
Modification date20141207
dbXrefs MIM : 154200
HGNC : HGNC
Ensembl : ENSG00000014641
HPRD : 01100
Vega : OTTHUMG00000129512
ProteinUniProt: P40925
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MDH1
BioGPS: 4190
Gene Expression Atlas: ENSG00000014641
The Human Protein Atlas: ENSG00000014641
PathwayNCI Pathway Interaction Database: MDH1
KEGG: MDH1
REACTOME: MDH1
ConsensusPathDB
Pathway Commons: MDH1
MetabolismMetaCyc: MDH1
HUMANCyc: MDH1
RegulationEnsembl's Regulation: ENSG00000014641
miRBase: chr2 :63,816,284-63,834,330
TargetScan: NM_001199111
cisRED: ENSG00000014641
ContextiHOP: MDH1
cancer metabolism search in PubMed: MDH1
UCL Cancer Institute: MDH1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MDH1 in cancer cell metabolism1. Lee SM, Kim JH, Cho EJ, Youn HD (2009) A nucleocytoplasmic malate dehydrogenase regulates p53 transcriptional activity in response to metabolic stress. Cell Death Differ 16: 738-748. doi: 10.1038/cdd.2009.5. go to article
2. Kounelakis MG, Zervakis ME, Giakos GC, Postma GJ, Buydens LM, et al. (2013) On the relevance of glycolysis process on brain gliomas. IEEE J Biomed Health Inform 17: 128-135. doi: 10.1109/TITB.2012.2199128. go to article

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Phenotypic Information for MDH1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MDH1
Familial Cancer Database: MDH1
* 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_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM 154200; gene.
Orphanet
DiseaseKEGG Disease: MDH1
MedGen: MDH1 (Human Medical Genetics with Condition)
ClinVar: MDH1
PhenotypeMGI: MDH1 (International Mouse Phenotyping Consortium)
PhenomicDB: MDH1

Mutations for MDH1
* 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 MDH1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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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
There's no copy number variation information in COSMIC data for this gene.

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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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr2:63834009-63834009p.K298R3
chr2:63832498-63832498p.V254I3
chr2:63826383-63826383p.F152S2
chr2:63824540-63824540p.I69I2
chr2:63826361-63826361p.P145A2
chr2:63832501-63832501p.R255G1
chr2:63822630-63822630p.D59G1
chr2:63834052-63834052p.K312N1
chr2:63826365-63826365p.S146F1
chr2:63833103-63833103p.D274N1

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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
# sample1  7  1 2  221  14 8
# mutation1  5  1 2  221  14 7
nonsynonymous SNV1  5  1 2  211  13 3
synonymous SNV            1    1 4
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
chr2:63834009p.K209R,MDH13
chr2:63824540p.I87I,MDH12
chr2:63834096p.A143S,MDH11
chr2:63832472p.K147N,MDH11
chr2:63834097p.S156Y,MDH11
chr2:63824541p.H164H,MDH11
chr2:63832497p.P22P,MDH11
chr2:63824624p.V165I,MDH11
chr2:63832498p.D69D,MDH11
chr2:63824675p.K206T,MDH11

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 MDH1 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 MDH1

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

ATP5C1,BOLA3,CCT4,CHAC2,COX5A,CPSF3,EPCAM,
FAM136A,FANCL,KCMF1,MDH1,MPHOSPH10,MTIF2,PNO1,
RAB1A,SF3B14,SNRPG,SUCLG1,TPRKB,UGP2,UQCRH
AP3S2,ATPAF1,MROH8,C22orf39,DLD,EIF2B3,ETFDH,
GPI,HOXA10,HSDL2,HSPB6,IDH3A,KIAA0408,MDH1,
PFKFB1,PHYH,RTN4,STRADB,SUCLA2,UGP2,YWHAG

ATP5C1,ATP5F1,ATP5G3,ATP5O,BOLA3,C2orf47,CCT4,
FAM96A,MDH1,MRPL35,MRPL44,MRPS9,MTX2,NDUFB3,
NDUFS3,ORC4,PRDX3,PSMD14,SDHD,SNRPG,SUCLG1
ARMC1,COQ3,CRYZL1,ESD,COX20,FRG1,FUNDC2,
KATNA1,MDH1,MOCS2,MYL6,NDUFA8,NDUFS5,PCMT1,
PRKRA,RWDD2B,SEPHS1,SNX3,SPOP,UQCRB,VDAC3
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 MDH1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P40925; -.
ChemistryChEMBL CHEMBL3560; -.
Organism-specific databasesPharmGKB PA30714; -.
Organism-specific databasesCTD 4190; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00157malate dehydrogenase 1, NAD (soluble)approved; nutraceuticalNADH
DB01907malate dehydrogenase 1, NAD (soluble)experimentalNicotinamide-Adenine-Dinucleotide
DB03461malate dehydrogenase 1, NAD (soluble)experimental2'-Monophosphoadenosine 5'-Diphosphoribose
DB00121malate dehydrogenase 1, NAD (soluble)approved; nutraceuticalBiotin


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Cross referenced IDs for MDH1
* 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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