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 PDHA1

Basic gene info.	Gene symbol	PDHA1
	Gene name	pyruvate dehydrogenase (lipoamide) alpha 1
	Synonyms	PDHA\|PDHAD\|PDHCE1A\|PHE1A
	Cytomap	UCSC genome browser: Xp22.1
	Genomic location	chrX :19362010-19379825
	Type of gene	protein-coding
	RefGenes	NM_000284.3, NM_001173454.1,NM_001173455.1,NM_001173456.1,
	Ensembl id	ENSG00000131828
	Description	PDHE1-A type Ipyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrialpyruvate dehydrogenase complex, E1-alpha polypeptide 1
	Modification date	20141207
dbXrefs	MIM : 300502
	HGNC : HGNC
	Ensembl : ENSG00000131828
	HPRD : 02420
	Vega : OTTHUMG00000021224
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PDHA1
	BioGPS: 5160
	Gene Expression Atlas: ENSG00000131828
	The Human Protein Atlas: ENSG00000131828
Pathway	NCI Pathway Interaction Database: PDHA1
	KEGG: PDHA1
	REACTOME: PDHA1
	ConsensusPathDB
	Pathway Commons: PDHA1
Metabolism	MetaCyc: PDHA1
	HUMANCyc: PDHA1
Regulation	Ensembl's Regulation: ENSG00000131828
	miRBase: chrX :19,362,010-19,379,825
	TargetScan: NM_000284
	cisRED: ENSG00000131828
Context	iHOP: PDHA1
	cancer metabolism search in PubMed: PDHA1
	UCL Cancer Institute: PDHA1
Assigned class in ccmGDB	C

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Phenotypic Information for PDHA1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PDHA1
	Familial Cancer Database: PDHA1

* 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_PYRUVATE_METABOLISM KEGG_BUTANOATE_METABOLISM REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE REACTOME_PYRUVATE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: PDHA1
	MedGen: PDHA1 (Human Medical Genetics with Condition)
	ClinVar: PDHA1
Phenotype	MGI: PDHA1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PDHA1

Mutations for PDHA1

* 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 PDHA1 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
AM746210	TMEM223	3	248	11	62559225	62559470	PDHA1	245	1004	X	19372607	19377866
BF694498	BOLA2	2	96	16	30076061	30078604	PDHA1	93	582	X	19372612	19377135
CB113851	SUB1	1	246	5	32585663	32591771	PDHA1	231	556	X	19373566	19377626

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=43)	Stat. for Synonymous SNVs (# total SNVs=17)

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
chr23:19368115-19368115	p.D60Y	3
chr23:19367444-19367444	p.L24L	3
chr23:19377730-19377730	p.R378C	3
chr23:19367443-19367443	p.L24P	2
chr23:19368163-19368163	p.L76L	2
chr23:19373600-19373600	p.G246D	2
chr23:19369427-19369427	p.G107D	2
chr23:19371280-19371280	p.V167M	1
chr23:19362177-19362177	p.V8I	1
chr23:19368114-19368114	p.E59E	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	3		9	1		3		2			4	4	1			1	2		8
# mutation	1	3		9	1		3		2			3	4	1			1	2		9
nonsynonymous SNV		2		6	1		3		2			3	3				1	1		7
synonymous SNV	1	1		3									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
chrX:19367444	p.L24L,PDHA1	3
chrX:19369427	p.G107D,PDHA1	3
chrX:19367443	p.L24P,PDHA1	2
chrX:19373600	p.C181F,PDHA1	2
chrX:19372640	p.G215D,PDHA1	2
chrX:19373844	p.L135L,PDHA1	1
chrX:19369418	p.E233K,PDHA1	1
chrX:19372657	p.G150R,PDHA1	1
chrX:19377039	p.R236K,PDHA1	1
chrX:19372671	p.Y161Y,PDHA1	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 PDHA1 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 PDHA1

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,AURKB,CMC2,CDC20,ECE2,KARS,KIF2C, MAGOH,NDUFAF4,PDCD5,PDHA1,PDSS1,PRDX4,PSMB2, PSMG1,PTTG1,SHFM1,TOMM5,TUBA1C,UQCRH,UQCRHL	ACAT1,ADHFE1,BCL2L13,CS,DLD,DLST,ETFDH, GPI,GPT2,KIAA0408,NDUFV3,PDHA1,PDK2,GATB, PFKFB1,PGM1,PHYH,PLIN5,RNF157,SLC2A4,SLC6A8

AIFM1,APOO,BRCC3,CASK,CCDC22,EBP,EMD, HCCS,HDAC8,HSD17B10,LAS1L,NDUFB11,PDHA1,JADE3, POLA1,RBBP7,SCML1,SMS,SUV39H1,TIMM8A,TSR2	AIFM1,CS,DARS2,DNAJC11,GJB2,GOT1,GSS, HMGB3,IARS2,IMMT,MCCC2,MIPEP,NDUFA10,NDUFS2, NDUFV1,PDHA1,PKP2,SLC35A4,STARD7,SUPV3L1,TUFM

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 PDHA1

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	pyruvate dehydrogenase (lipoamide) alpha 1	approved; nutraceutical	NADH

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Cross referenced IDs for PDHA1

* 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