Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 MDH2

Basic gene info.	Gene symbol	MDH2
	Gene name	malate dehydrogenase 2, NAD (mitochondrial)
	Synonyms	M-MDH\|MDH\|MGC:3559\|MOR1
	Cytomap	UCSC genome browser: 7cen-q22
	Genomic location	chr7 :75677392-75695930
	Type of gene	protein-coding
	RefGenes	NM_001282403.1, NM_001282404.1,NM_005918.3,NR_104165.1,
	Ensembl id	ENSG00000262847
	Description	malate dehydrogenase, mitochondrial
	Modification date	20141207
dbXrefs	MIM : 154100
	HGNC : HGNC
	Ensembl : ENSG00000146701
	HPRD : 01099
	Vega : OTTHUMG00000023827
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MDH2
	BioGPS: 4191
	Gene Expression Atlas: ENSG00000262847
	The Human Protein Atlas: ENSG00000262847
Pathway	NCI Pathway Interaction Database: MDH2
	KEGG: MDH2
	REACTOME: MDH2
	ConsensusPathDB
	Pathway Commons: MDH2
Metabolism	MetaCyc: MDH2
	HUMANCyc: MDH2
Regulation	Ensembl's Regulation: ENSG00000262847
	miRBase: chr7 :75,677,392-75,695,930
	TargetScan: NM_001282403
	cisRED: ENSG00000262847
Context	iHOP: MDH2
	cancer metabolism search in PubMed: MDH2
	UCL Cancer Institute: MDH2
Assigned class in ccmGDB	C

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Phenotypic Information for MDH2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic 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

Others
OMIM
Orphanet
Disease	KEGG Disease: MDH2
	MedGen: MDH2 (Human Medical Genetics with Condition)
	ClinVar: MDH2
Phenotype	MGI: MDH2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	MDH2	chr7	75689245	75689265	STK3	chr8	99623537	99623557

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MDH2 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BP259062	MDH2	1	234	7	75677424	75684260	LOC100507412	229	448	?	109556	109774
BF794536	MDH2	24	102	7	75695601	75695679	MDH2	91	340	7	75695658	75695908

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

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SNV 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

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Somatic 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.

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Top 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 position	Mutation(aa)	Unique sampleID count
chr7:75677504-75677504	p.A9V	9
chr7:75686766-75686766	p.G92C	2
chr7:75692906-75692906	p.S210C	2
chr7:75687331-75687331	p.A122S	2
chr7:75693664-75693664	p.P214L	2
chr7:75694234-75694234	p.T283M	2
chr7:75689759-75689759	p.I166I	1
chr7:75693701-75693701	p.L226L	1
chr7:75686754-75686754	p.D88Y	1
chr7:75694266-75694266	p.L294F	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		1		4			1					3	2	2	1		8	1		5
# mutation		1		4			1					3	2	2	1		8	1		5
nonsynonymous SNV		1		3								2	1	2	1		4	1		3
synonymous SNV				1			1					1	1				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])

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Top 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 Position	Mutation(aa)	Unique sampleID count
chr7:75695601	p.K255R,MDH2	2
chr7:75693708	p.I43I,MDH2	1
chr7:75687295	p.F291F,MDH2	1
chr7:75694157	p.I59I,MDH2	1
chr7:75687336	p.V62M,MDH2	1
chr7:75694217	p.I67I,MDH2	1
chr7:75689711	p.G157G,MDH2	1
chr7:75694218	p.S168C,MDH2	1
chr7:75684173	p.G31V,MDH2	1
chr7:75689759	p.P172L,MDH2	1

Other 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

Copy 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]

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Gene Expression for MDH2

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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 MDH2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00157	malate dehydrogenase 2, NAD (mitochondrial)	approved; nutraceutical	NADH
DB04272	malate dehydrogenase 2, NAD (mitochondrial)	experimental	Citric Acid
DB00121	malate dehydrogenase 2, NAD (mitochondrial)	approved; nutraceutical	Biotin

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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