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 SLC27A1

Basic gene info.	Gene symbol	SLC27A1
	Gene name	solute carrier family 27 (fatty acid transporter), member 1
	Synonyms	ACSVL5\|FATP\|FATP1
	Cytomap	UCSC genome browser: 19p13.11
	Genomic location	chr19 :17581299-17616977
	Type of gene	protein-coding
	RefGenes	NM_198580.1,
	Ensembl id	ENSG00000130304
	Description	FATP-1fatty acid transport protein 1long-chain fatty acid transport protein 1solute carrier family 27 member 1
	Modification date	20141207
dbXrefs	MIM : 600691
	HGNC : HGNC
	Ensembl : ENSG00000130304
	HPRD : 11863
	Vega : OTTHUMG00000182878
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLC27A1
	BioGPS: 376497
	Gene Expression Atlas: ENSG00000130304
	The Human Protein Atlas: ENSG00000130304
Pathway	NCI Pathway Interaction Database: SLC27A1
	KEGG: SLC27A1
	REACTOME: SLC27A1
	ConsensusPathDB
	Pathway Commons: SLC27A1
Metabolism	MetaCyc: SLC27A1
	HUMANCyc: SLC27A1
Regulation	Ensembl's Regulation: ENSG00000130304
	miRBase: chr19 :17,581,299-17,616,977
	TargetScan: NM_198580
	cisRED: ENSG00000130304
Context	iHOP: SLC27A1
	cancer metabolism search in PubMed: SLC27A1
	UCL Cancer Institute: SLC27A1
Assigned class in ccmGDB	C

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Phenotypic Information for SLC27A1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SLC27A1
	Familial Cancer Database: SLC27A1

* 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: SLC27A1
	MedGen: SLC27A1 (Human Medical Genetics with Condition)
	ClinVar: SLC27A1
Phenotype	MGI: SLC27A1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SLC27A1

Mutations for SLC27A1

* 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 SLC27A1 related fusion information.

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

BI009992

ZDHHC24

273

66310112

66310383

SLC27A1

266

389

17615616

17615741

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=47)	Stat. for Synonymous SNVs (# total SNVs=17)

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
chr19:17612144-17612144	p.A567T	4
chr19:17615314-17615314	p.R612C	2
chr19:17608117-17608117	p.R350R	2
chr19:17611525-17611525	p.D492E	2
chr19:17597398-17597398	p.R65H	2
chr19:17598003-17598003	p.H195Y	1
chr19:17611318-17611318	p.L450I	1
chr19:17599834-17599834	p.G302W	1
chr19:17611637-17611637	p.R530C	1
chr19:17597443-17597443	p.R80H	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		7	1		3		2	1		5	2				4	6		14
# mutation	2	2		6	1		3		2	1		5	2				4	6		16
nonsynonymous SNV		1		3	1		1		2	1		3	1				2	4		10
synonymous SNV	2	1		3			2					2	1				2	2		6

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
chr19:17611658	p.A645T	2
chr19:17615413	p.V537M	2
chr19:17608117	p.H195Y	1
chr19:17615329	p.V424V	1
chr19:17611209	p.A554V	1
chr19:17597672	p.S264I	1
chr19:17608160	p.R433Q	1
chr19:17615340	p.P559P	1
chr19:17611306	p.A282A	1
chr19:17597695	p.Q443Q	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 SLC27A1 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 SLC27A1

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


ABTB1,ACBD4,C16orf86,C21orf2,CCDC130,CCDC159,CIRBP, CRTC1,MVB12A,GLTSCR2,LOC284440,PHF1,POLL,QTRT1, RAB11B,SIX5,SLC27A1,SSBP4,TNFSF12,UBXN6,ZDHHC1	BTBD2,VPS51___IFT46,C12orf10,BRAT1,NELFB,CPSF3L,FUZ, MRPS2,NFKBIL1,PEX14,POLL,PRKCSH,QTRT1,RFNG, RFXANK,SIX5,SLC27A1,SPNS1,SPSB3,TMEM161A,XAB2

ARHGEF1,CCDC114,CHPF,DBN1,ITGA10,LMF1,LOC100127888, LOC284440,LZTS2,MC1R,PHF1,PIAS3,POLR3GL,PRX, SHB,SHC2,SHF,SLC27A1,STXBP1,TLR5,VAT1	ADAMTS10,C2CD2,C2orf81,EPOR,GPRC5B,HDAC7,IFFO1, IQSEC1,KCND1,LEPRE1,LOXL3,LRRC2,MAN1C1,MAP3K12, MXRA8,NCKAP5L,OLFML1,PTPRS,RNF112,SIX5,SLC27A1

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 SLC27A1

There's no related Drug.

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Cross referenced IDs for SLC27A1

* 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