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 L2HGDH

Basic gene info.	Gene symbol	L2HGDH
	Gene name	L-2-hydroxyglutarate dehydrogenase
	Synonyms	C14orf160
	Cytomap	UCSC genome browser: 14q21.3
	Genomic location	chr14 :50709151-50778947
	Type of gene	protein-coding
	RefGenes	NM_024884.2,
	Ensembl id	ENSG00000087299
	Description	2-hydroxyglutarate dehydrogenaseL-2-hydroxyglutarate dehydrogenase, mitochondrialL-alpha-hydroxyglutarate dehydrogenasealpha-hydroxyglutarate oxidoreductasealpha-ketoglutarate reductaseduranin
	Modification date	20141207
dbXrefs	MIM : 609584
	HGNC : HGNC
	Ensembl : ENSG00000087299
	HPRD : 12640
	Vega : OTTHUMG00000140289
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_L2HGDH
	BioGPS: 79944
	Gene Expression Atlas: ENSG00000087299
	The Human Protein Atlas: ENSG00000087299
Pathway	NCI Pathway Interaction Database: L2HGDH
	KEGG: L2HGDH
	REACTOME: L2HGDH
	ConsensusPathDB
	Pathway Commons: L2HGDH
Metabolism	MetaCyc: L2HGDH
	HUMANCyc: L2HGDH
Regulation	Ensembl's Regulation: ENSG00000087299
	miRBase: chr14 :50,709,151-50,778,947
	TargetScan: NM_024884
	cisRED: ENSG00000087299
Context	iHOP: L2HGDH
	cancer metabolism search in PubMed: L2HGDH
	UCL Cancer Institute: L2HGDH
Assigned class in ccmGDB	C

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Phenotypic Information for L2HGDH(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: L2HGDH
	Familial Cancer Database: L2HGDH

* 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_BUTANOATE_METABOLISM REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

Others
OMIM
Orphanet
Disease	KEGG Disease: L2HGDH
	MedGen: L2HGDH (Human Medical Genetics with Condition)
	ClinVar: L2HGDH
Phenotype	MGI: L2HGDH (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: L2HGDH

Mutations for L2HGDH

* 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

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	L2HGDH	chr14	50718444	50718464	L2HGDH	chr14	50719361	50719381
ovary	L2HGDH	chr14	50718444	50718464	L2HGDH	chr14	50719363	50719383
ovary	L2HGDH	chr14	50770751	50770771	L2HGDH	chr14	50762106	50762126

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 L2HGDH 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
BE908214	L2HGDH	1	315	14	50712522	50712835	KRT19	309	362	17	39679869	39679922
DA137061	L2HGDH	1	68	14	50712199	50712266	MBP	68	519	18	74696800	74729012
AF335584	L2HGDH	1	100	14	50710170	50710269	PDGFD	99	1828	11	103779888	104034738
AW300486	L2HGDH	1	343	14	50712259	50712601	KIAA1191	339	456	5	175774557	175774674

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=32)	Stat. for Synonymous SNVs (# total SNVs=6)

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
chr14:50778816-50778816	p.L18R	5
chr14:50750699-50750699	p.V198G	3
chr14:50760867-50760867	p.Q169L	2
chr14:50736035-50736035	p.R251P	2
chr14:50713876-50713876	p.R431H	2
chr14:50732175-50732175	p.S366F	2
chr14:50734547-50734547	p.V330I	1
chr14:50736014-50736014	p.C258Y	1
chr14:50713819-50713819	p.S450F	1
chr14:50778849-50778849	p.Y7C	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			3			3		1			5		2			4	3		4
# mutation	1			3			3		1			5		2			4	3		4
nonsynonymous SNV	1			2			3		1			4		2			3	1		4
synonymous SNV				1								1					1	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
chr14:50713876	p.R251P	2
chr14:50736035	p.R431H	2
chr14:50734574	p.R265H	1
chr14:50760887	p.X464X	1
chr14:50713777	p.V255L	1
chr14:50734600	p.S450F	1
chr14:50760895	p.E223K	1
chr14:50713819	p.E417K	1
chr14:50735964	p.F206F	1
chr14:50769692	p.Q169L	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 L2HGDH 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 L2HGDH

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


ARF6,ATP5S,DNAAF2,MIS18BP1,DDHD1,EXOC5,FANCM, GMFB,GNPNAT1,L2HGDH,NAA30,OR4A15,POLE2,PSMC6, NEMF,SOCS4,SOS2,STYX,TMX1,TXNDC16,WDHD1	ALPK3,ATP5B,TCAIM,CECR2,COX10,HECTD1,VWA8, L2HGDH,LOC729082,LYRM7,NDUFS1,NPEPPS,OXNAD1,PAIP2B, PDHX,PPARA,PTCD3,SATB1,TARSL2,UQCRC2,ZYG11B

DNAAF2,CPSF2,DLGAP5,EIF2S1,FANCM,FCF1,G2E3, GMFB,GNPNAT1,KIAA0391,KIAA0586,L2HGDH,MTHFD1,AP5M1, POLE2,PRMT5,SUPT16H,TDP1,TMX1,TRMT5,WDHD1	ACTL6A,DCLRE1A,DNAJA3,G2E3,GMNN,HN1L,L2HGDH, MRPS35,NARS2,PRMT3,PTCD3,PUS7L,RBBP4,RPE, SHQ1,TBCCD1,TFAM,TFDP1,TMEM5,TRNT1,ZC3H8

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 L2HGDH

There's no related Drug.

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Cross referenced IDs for L2HGDH

* 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