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 DLD

Basic gene info.	Gene symbol	DLD
	Gene name	dihydrolipoamide dehydrogenase
	Synonyms	DLDD\|DLDH\|E3\|GCSL\|LAD\|PHE3
	Cytomap	UCSC genome browser: 7q31-q32
	Genomic location	chr7 :107531585-107561643
	Type of gene	protein-coding
	RefGenes	NM_000108.4, NM_001289750.1,NM_001289751.1,NM_001289752.1,
	Ensembl id	ENSG00000091140
	Description	E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complexdiaphorasedihydrolipoyl dehydrogenase, mitochondrialglycine cleavage system L proteinglycine cleavage system protein Llipoamide deh
	Modification date	20141207
dbXrefs	MIM : 238331
	HGNC : HGNC
	Ensembl : ENSG00000091140
	HPRD : 02006
	Vega : OTTHUMG00000154813
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DLD
	BioGPS: 1738
	Gene Expression Atlas: ENSG00000091140
	The Human Protein Atlas: ENSG00000091140
Pathway	NCI Pathway Interaction Database: DLD
	KEGG: DLD
	REACTOME: DLD
	ConsensusPathDB
	Pathway Commons: DLD
Metabolism	MetaCyc: DLD
	HUMANCyc: DLD
Regulation	Ensembl's Regulation: ENSG00000091140
	miRBase: chr7 :107,531,585-107,561,643
	TargetScan: NM_000108
	cisRED: ENSG00000091140
Context	iHOP: DLD
	cancer metabolism search in PubMed: DLD
	UCL Cancer Institute: DLD
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: DLD
	Familial Cancer Database: DLD

* 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_GLYCOLYSIS_GLUCONEOGENESIS KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM KEGG_PYRUVATE_METABOLISM REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_PYRUVATE_METABOLISM

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

Mutations for DLD

* 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
breast	DLD	chr7	107535122	107535122	NRCAM	chr7	107818574	107818574
ovary	DLD	chr7	107551266	107551286		chr7	107374232	107374252

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 DLD 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
CV348467	IKBKB	1	314	8	42181155	42181470	DLD	304	497	7	107557272	107557773
BG952037	DLD	9	114	7	107560077	107560184	SURF4	102	298	9	136228391	136228587

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=33)	Stat. for Synonymous SNVs (# total SNVs=7)

Stat. for Deletions (# total SNVs=3)	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
chr7:107557813-107557813	p.A381D	3
chr7:107558487-107558487	p.G452A	2
chr7:107558488-107558488	p.G452G	2
chr7:107545876-107545876	p.G170D	2
chr7:107557721-107557721	p.I350M	2
chr7:107557761-107557761	p.H364Y	2
chr7:107557346-107557346	p.G328E	2
chr7:107545828-107545828	p.G154E	1
chr7:107546788-107546788	p.G220V	1
chr7:107557386-107557386	p.T341T	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	1	1	5	2				3	1	1	9	2				2	4		4
# mutation	1	1	1	4	2				5	1	1	10	2				2	4		4
nonsynonymous SNV	1	1	1	2	2				4	1	1	8	1				2	3		4
synonymous SNV				2					1			2	1					1

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
chr7:107545876	p.G71D,DLD	2
chr7:107558488	p.G353G,DLD	2
chr7:107546743	p.T177K,DLD	1
chr7:107557761	p.I86T,DLD	1
chr7:107543968	p.S193F,DLD	1
chr7:107555972	p.I86M,DLD	1
chr7:107557789	p.K221M,DLD	1
chr7:107545454	p.D6Y,DLD	1
chr7:107556003	p.P234S,DLD	1
chr7:107558381	p.A31E,DLD	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 DLD 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 DLD

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


CBLL1,COG5,DLD,DUS4L,GCC1,GTPBP10,LRPPRC, LUZP6,METTL2B,MRPL19,NUP205,ORC5,PMPCB,PNPLA8, PSMC2,PUS7,RINT1,SLC25A13,THAP5,TNPO3,UBE3C	ACAT1,AK3,ATPAF1,DLD,ETFDH,GHITM,GNPAT, HADHB,HOXA10,HSDL2,HSPB6,PDHX,PGM1,PHYH, RDX,RRAGD,SLC2A4,SOX6,STRADB,SUCLA2,TBX15

ARMC10,CHCHD3,COG5,CYCS,DLD,FAM185A,GHITM, GPD1L,GTPBP10,LRPPRC,MDH2,MRPS33,NDUFA5,ORC5, PEX1,PMPCB,RINT1,SLC25A13,SUCLG2,SYPL1,ZNF800	AIFM2,ANKRD13C,CA2,CYCS,DLAT,DLD,ETNK1, FH,GCLM,GHITM,LRP12,ME2,MIER1,NAA50, NDUFS1,RTN4IP1,SLC25A33,STK39,UBE2K,UGDH,VPS26A

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 DLD

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	dihydrolipoamide dehydrogenase	approved; nutraceutical	NADH
DB01907	dihydrolipoamide dehydrogenase	experimental	Nicotinamide-Adenine-Dinucleotide
DB03147	dihydrolipoamide dehydrogenase	experimental	Flavin-Adenine Dinucleotide

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Cross referenced IDs for DLD

* 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