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 MDH1

Basic gene info.	Gene symbol	MDH1
	Gene name	malate dehydrogenase 1, NAD (soluble)
	Synonyms	HEL-S-32\|MDH-s\|MDHA\|MGC:1375\|MOR2
	Cytomap	UCSC genome browser: 2p13.3
	Genomic location	chr2 :63816284-63834330
	Type of gene	protein-coding
	RefGenes	NM_001199111.1, NM_001199112.1,NM_005917.3,
	Ensembl id	ENSG00000014641
	Description	cytosolic malate dehydrogenasediiodophenylpyruvate reductaseepididymis secretory protein Li 32malate dehydrogenase, cytoplasmicsoluble malate dehydrogenase
	Modification date	20141207
dbXrefs	MIM : 154200
	HGNC : HGNC
	Ensembl : ENSG00000014641
	HPRD : 01100
	Vega : OTTHUMG00000129512
Protein	UniProt: P40925 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MDH1
	BioGPS: 4190
	Gene Expression Atlas: ENSG00000014641
	The Human Protein Atlas: ENSG00000014641
Pathway	NCI Pathway Interaction Database: MDH1
	KEGG: MDH1
	REACTOME: MDH1
	ConsensusPathDB
	Pathway Commons: MDH1
Metabolism	MetaCyc: MDH1
	HUMANCyc: MDH1
Regulation	Ensembl's Regulation: ENSG00000014641
	miRBase: chr2 :63,816,284-63,834,330
	TargetScan: NM_001199111
	cisRED: ENSG00000014641
Context	iHOP: MDH1
	cancer metabolism search in PubMed: MDH1
	UCL Cancer Institute: MDH1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MDH1 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_PYRUVATE_METABOLISM KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM	154200; gene.
Orphanet
Disease	KEGG Disease: MDH1
	MedGen: MDH1 (Human Medical Genetics with Condition)
	ClinVar: MDH1
Phenotype	MGI: MDH1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MDH1 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
BM741416	KPNB1	1	432	17	45755440	45757968	MDH1	433	614	2	63816113	63822571
BM751800	KPNB1	1	432	17	45755440	45757968	MDH1	433	599	2	63816113	63821720
BM768103	KPNB1	1	432	17	45755440	45757968	MDH1	433	596	2	63816113	63821717
BM745157	KPNB1	1	431	17	45755440	45757968	MDH1	432	598	2	63816113	63821720
BM741420	KPNB1	1	431	17	45755440	45757968	MDH1	432	623	2	63816113	63822581
CK003575	MDH1	4	53	2	63816097	63816146	CTNNA1	53	622	5	138269887	138270464
BM768064	KPNB1	1	433	17	45755440	45757968	MDH1	434	598	2	63816113	63821718
AA092172	MAGED2	1	99	X	54834178	54837913	MDH1	94	276	2	63831921	63832514
BE709622	MDH1	8	67	2	63831845	63831904	LRTOMT	65	249	11	71796442	71796626
AA315813	SMPD4	1	220	2	130932487	130939151	MDH1	219	495	2	63821620	63824707
BM767348	KPNB1	1	432	17	45755440	45757968	MDH1	433	596	2	63816113	63821717
BG290076	MDH1	39	308	2	63831925	63833146	MDH1	302	744	2	63831899	63834120
AW951984	SMPD4	1	219	2	130932487	130939150	MDH1	218	333	2	63821620	63824547

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

There's no copy number variation information in COSMIC data for this gene.

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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=5

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Somatic 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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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
chr2:63834009-63834009	p.K298R	3
chr2:63832498-63832498	p.V254I	3
chr2:63826361-63826361	p.P145A	2
chr2:63826383-63826383	p.F152S	2
chr2:63824540-63824540	p.I69I	2
chr2:63824541-63824541	p.A70T	1
chr2:63826418-63826418	p.K164E	1
chr2:63834010-63834010	p.K298N	1
chr2:63824624-63824624	p.E97D	1
chr2:63832413-63832413	p.?	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=3

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			7			1		2			2	2	1			1	4		8
# mutation	1			5			1		2			2	2	1			1	4		7
nonsynonymous SNV	1			5			1		2			2	1	1			1	3		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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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
chr2:63834009	p.K209R,MDH1	3
chr2:63824540	p.I87I,MDH1	2
chr2:63824683	p.K32N,MDH1	1
chr2:63824696	p.A238D,MDH1	1
chr2:63834039	p.F63L,MDH1	1
chr2:63826382	p.A238A,MDH1	1
chr2:63834040	p.F63S,MDH1	1
chr2:63826383	p.D127N,MDH1	1
chr2:63834042	p.A143S,MDH1	1
chr2:63821630	p.K147N,MDH1	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 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

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


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

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 MDH1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P40925; -.
Chemistry	ChEMBL	CHEMBL3560; -.
Organism-specific databases	PharmGKB	PA30714; -.
Organism-specific databases	CTD	4190; -.

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 1, NAD (soluble)	approved; nutraceutical	NADH
DB01907	malate dehydrogenase 1, NAD (soluble)	experimental	Nicotinamide-Adenine-Dinucleotide
DB03461	malate dehydrogenase 1, NAD (soluble)	experimental	2'-Monophosphoadenosine 5'-Diphosphoribose
DB00121	malate dehydrogenase 1, NAD (soluble)	approved; nutraceutical	Biotin

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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