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 ATP5A1

Basic gene info.	Gene symbol	ATP5A1
	Gene name	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle
	Synonyms	ATP5A\|ATP5AL2\|ATPM\|COXPD22\|HEL-S-123m\|MC5DN4\|MOM2\|OMR\|ORM\|hATP1
	Cytomap	UCSC genome browser: 18q21
	Genomic location	chr18 :43664109-43678319
	Type of gene	protein-coding
	RefGenes	NM_001001935.2, NM_001001937.1,NM_001257334.1,NM_001257335.1,NM_004046.5,
	Ensembl id	ENSG00000152234
	Description	ATP synthase alpha chain, mitochondrialATP synthase subunit alpha, mitochondrialATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscleATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, iso
	Modification date	20141207
dbXrefs	MIM : 164360
	HGNC : HGNC
	Ensembl : ENSG00000152234
	HPRD : 01258
	Vega : OTTHUMG00000132637
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ATP5A1
	BioGPS: 498
	Gene Expression Atlas: ENSG00000152234
	The Human Protein Atlas: ENSG00000152234
Pathway	NCI Pathway Interaction Database: ATP5A1
	KEGG: ATP5A1
	REACTOME: ATP5A1
	ConsensusPathDB
	Pathway Commons: ATP5A1
Metabolism	MetaCyc: ATP5A1
	HUMANCyc: ATP5A1
Regulation	Ensembl's Regulation: ENSG00000152234
	miRBase: chr18 :43,664,109-43,678,319
	TargetScan: NM_001001935
	cisRED: ENSG00000152234
Context	iHOP: ATP5A1
	cancer metabolism search in PubMed: ATP5A1
	UCL Cancer Institute: ATP5A1
Assigned class in ccmGDB	C

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Phenotypic Information for ATP5A1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ATP5A1
	Familial Cancer Database: ATP5A1

* 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
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: ATP5A1
	MedGen: ATP5A1 (Human Medical Genetics with Condition)
	ClinVar: ATP5A1
Phenotype	MGI: ATP5A1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ATP5A1

Mutations for ATP5A1

* 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 ATP5A1 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
DA148364	ATP5A1	1	241	18	43671770	43678251	NEFL	236	569	8	24813798	24814131
BQ640716	ATP5A1	9	315	18	43666118	43667066	ATP5A1	310	584	18	43668157	43669829
DA496129	ATP5A1	1	452	18	43669885	43678262	TSC22D1	447	555	13	45149664	45149772
AU143199	PSMC5	1	210	17	61908875	61909296	ATP5A1	210	695	18	43669875	43678287
BC014208	HUWE1	10	1432	X	53587310	53600869	ATP5A1	1433	3280	18	43664115	43678250
BP259811	ATP5A1	1	272	18	43671735	43678247	MYL12A	273	488	18	3252279	3253401
BC007607	ATP5A1	38	1874	18	43664115	43678239	BAIAP2L1	1875	2744	7	98015039	98015908
BC001637	HUWE1	1	1423	X	53587310	53600869	ATP5A1	1424	3271	18	43664115	43678250
DA521883	LOC100507412	1	155	?	112025	112179	ATP5A1	156	546	18	43673145	43678262

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=6

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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=12)

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
chr18:43664328-43664328	p.A528S	6
chr18:43666116-43666116	p.G464G	2
chr18:43666156-43666156	p.S451C	2
chr18:43668065-43668065	p.?	2
chr18:43669645-43669645	p.I179M	2
chr18:43666404-43666404	p.G411G	2
chr18:43671703-43671703	p.H85L	2
chr18:43671728-43671728	p.I77F	2
chr18:43666464-43666464	p.?	2
chr18:43668217-43668217	p.T219T	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	2		10	2		1		2	1		5	3	1		1	2	3		7
# mutation	1	2		10	2		1		2	1		5	3	1		1	2	3		10
nonsynonymous SNV	1	1		7	1				2	1		3	3	1		1	1	1		8
synonymous SNV		1		3	1		1					2					1	2		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
chr18:43671703	p.H35R,ATP5A1	2
chr18:43666116	p.G414G,ATP5A1	2
chr18:43666423	p.P332A,ATP5A1	1
chr18:43671809	p.R119H,ATP5A1	1
chr18:43667414	p.P15H,ATP5A1	1
chr18:43669872	p.I320I,ATP5A1	1
chr18:43666432	p.E94K,ATP5A1	1
chr18:43675021	p.G283G,ATP5A1	1
chr18:43668121	p.P91P,ATP5A1	1
chr18:43669913	p.A268D,ATP5A1	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 ATP5A1 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 ATP5A1

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


ATP5A1,TPGS2,C18orf21,RBFA,C18orf25,TIMM21,DYM, FECH,HAUS1,HDHD2,IER3IP1,INO80C,NARS,PIAS2, PIK3C3,RPL17,SEC11C,SMAD2,TXNL1,TXNL4A,ZNF271P	ATP5A1,ATP5B,COQ3,COQ9,COX10,COX5A,CYC1, FH,GYS1,IMMT,MDH2,NDUFA9,NDUFB3,NDUFS2, NDUFS3,NDUFV2,POLDIP2,SLC25A3,UQCR10,UQCRC1,UQCRFS1

ATP5A1,ATP5B,ATPAF2,RBFA,TIMM21,C1QBP,CNDP2, CXXC1,DLST,EIF4A1,EIF5AL1,ELAC2,FECH,IER3IP1, ME2,MPDU1,NARS,PIAS2,SCO1,TXNL1,TXNL4A	ATP5A1,ATP5B,ATP5C1,ATP5F1,ATP5G3,C2orf47,ETFA, FH,IDH3B,MDH2,MRPL35,MTCH2,NDUFA9,NDUFS3, PPIA,RTN4IP1,SDHB,UQCR10,UQCRC2,UQCRFS1,UQCRHL

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 ATP5A1

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
DB04216	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	experimental	Quercetin
DB07384	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	experimental	1-ACETYL-2-CARBOXYPIPERIDINE
DB07394	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	experimental	AUROVERTIN B
DB08399	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	experimental	PICEATANNOL
DB08629	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	experimental	N1-(2-AMINO-4-METHYLPENTYL)OCTAHYDRO-PYRROLO[1,2-A] PYRIMIDINE

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Cross referenced IDs for ATP5A1

* 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