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 SLC27A5

Basic gene info.	Gene symbol	SLC27A5
	Gene name	solute carrier family 27 (fatty acid transporter), member 5
	Synonyms	ACSB\|ACSVL6\|BACS\|BAL\|FACVL3\|FATP-5\|FATP5\|VLACSR\|VLCS-H2\|VLCSH2
	Cytomap	UCSC genome browser: 19q13.43
	Genomic location	chr19 :59009699-59023432
	Type of gene	protein-coding
	RefGenes	NM_012254.2,
	Ensembl id	ENSG00000083807
	Description	BA-CoA ligaseVLACS-relatedbile acid-CoA ligasebile acyl-CoA synthetasecholate--CoA ligasefatty acid transport protein 5fatty-acid-Coenzyme A ligase, very long-chain 3solute carrier family 27 member 5very long-chain acyl-CoA synthetase homolog 2ve
	Modification date	20141207
dbXrefs	MIM : 603314
	HGNC : HGNC
	Ensembl : ENSG00000083807
	HPRD : 04499
	Vega : OTTHUMG00000183543
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLC27A5
	BioGPS: 10998
	Gene Expression Atlas: ENSG00000083807
	The Human Protein Atlas: ENSG00000083807
Pathway	NCI Pathway Interaction Database: SLC27A5
	KEGG: SLC27A5
	REACTOME: SLC27A5
	ConsensusPathDB
	Pathway Commons: SLC27A5
Metabolism	MetaCyc: SLC27A5
	HUMANCyc: SLC27A5
Regulation	Ensembl's Regulation: ENSG00000083807
	miRBase: chr19 :59,009,699-59,023,432
	TargetScan: NM_012254
	cisRED: ENSG00000083807
Context	iHOP: SLC27A5
	cancer metabolism search in PubMed: SLC27A5
	UCL Cancer Institute: SLC27A5
Assigned class in ccmGDB	C

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Phenotypic Information for SLC27A5(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SLC27A5
	Familial Cancer Database: SLC27A5

* 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_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: SLC27A5
	MedGen: SLC27A5 (Human Medical Genetics with Condition)
	ClinVar: SLC27A5
Phenotype	MGI: SLC27A5 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SLC27A5

Mutations for SLC27A5

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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	SLC27A5	chr19	59019124	59019144	MZF1	chr19	59077200	59077220

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 SLC27A5 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
AA457551	SLC27A5	1	56	19	59014991	59015502	ESRRG	40	74	1	216730758	216731096
DA285853	SNHG1	2	59	11	62621379	62621436	SLC27A5	47	485	19	59022932	59023364

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=9

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=52)	Stat. for Synonymous SNVs (# total SNVs=16)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=1)

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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
chr19:59010865-59010865	p.T554I	4
chr19:59012030-59012030	p.N409T	3
chr19:59010864-59010864	p.T554T	3
chr19:59010864-59010865	p.T554I	2
chr19:59022196-59022196	p.L264M	2
chr19:59023174-59023174	p.M50T	2
chr19:59022806-59022806	p.E173Q	2
chr19:59023203-59023203	p.P40P	2
chr19:59010878-59010878	p.R550C	2
chr19:59021289-59021289	p.D328N	2

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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=6

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	4	3		9			3		3			4	6	2			13	6		5
# mutation	4	3		9			4		3			4	6	2			11	8		5
nonsynonymous SNV	3	2		8			2		2			2	4	1			4	5		3
synonymous SNV	1	1		1			2		1			2	2	1			7	3		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
chr19:59010864	p.T554T	4
chr19:59010865	p.T554I	2
chr19:59010878	p.R550C	2
chr19:59011000	p.F555F	1
chr19:59022207	p.D398N	1
chr19:59012064	p.T308A	1
chr19:59023253	p.V24M	1
chr19:59010056	p.E397E	1
chr19:59021257	p.P302P	1
chr19:59011001	p.P393P	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 SLC27A5 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 SLC27A5

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


ATP5D,UQCC3,C19orf70,DPM3,HSPBP1,NDUFA3,NHP2, RPL18,RPL28,RPL8,RPS11,RPS19,RPS5,RPS9, RUVBL2,SLC27A5,SNRPD2,UBE2M,ZNF524,ZNF579,ZNF593	APRT,CNPY2,COQ4,EXOSC5,HMG20B,NME2,NPM3, RPL13,RPL13A,RPL18,RPL18A,RPL36,RPL7A,RPL8, RPS15,RPS19,RPS3,RPS9,RUVBL2,SLC27A5,TSC22D4

BCL2L12,UQCC3,C7orf55,RPP25L,FBL,ISOC2,MRPL12, MRPL4,MRPS12,POP7,PRMT1,RPL18,RPS19,RUVBL2, SDHAF1,SIVA1,SLC27A5,SNRPD2,TIMM50,UBE2M,UBE2S	ADH5,C7orf25,C7orf60,CCDC53,CXCL5,FBXO8,FLOT1, GSTA3,IL12A,LEPROT,LHX8,LOC400759,PAQR9,PER4, RAD51B,RPL39L,SCGB1D4,SEPT14,SLC27A5,TMEM155,ZNF658

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 SLC27A5

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
DB00145	solute carrier family 27 (fatty acid transporter), member 5	approved; nutraceutical	Glycine

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Cross referenced IDs for SLC27A5

* 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