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 symbolSLC27A5
Gene namesolute carrier family 27 (fatty acid transporter), member 5
SynonymsACSB|ACSVL6|BACS|BAL|FACVL3|FATP-5|FATP5|VLACSR|VLCS-H2|VLCSH2
CytomapUCSC genome browser: 19q13.43
Genomic locationchr19 :59009699-59023432
Type of geneprotein-coding
RefGenesNM_012254.2,
Ensembl idENSG00000083807
DescriptionBA-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 date20141207
dbXrefs MIM : 603314
HGNC : HGNC
Ensembl : ENSG00000083807
HPRD : 04499
Vega : OTTHUMG00000183543
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLC27A5
BioGPS: 10998
Gene Expression Atlas: ENSG00000083807
The Human Protein Atlas: ENSG00000083807
PathwayNCI Pathway Interaction Database: SLC27A5
KEGG: SLC27A5
REACTOME: SLC27A5
ConsensusPathDB
Pathway Commons: SLC27A5
MetabolismMetaCyc: SLC27A5
HUMANCyc: SLC27A5
RegulationEnsembl's Regulation: ENSG00000083807
miRBase: chr19 :59,009,699-59,023,432
TargetScan: NM_012254
cisRED: ENSG00000083807
ContextiHOP: SLC27A5
cancer metabolism search in PubMed: SLC27A5
UCL Cancer Institute: SLC27A5
Assigned class in ccmGDBC

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Phenotypic Information for SLC27A5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SLC27A5
MedGen: SLC27A5 (Human Medical Genetics with Condition)
ClinVar: SLC27A5
PhenotypeMGI: SLC27A5 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovarySLC27A5chr195901912459019144MZF1chr195907720059077220
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SLC27A5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA457551SLC27A5156195901499159015502ESRRG40741216730758216731096
DA285853SNHG1259116262137962621436SLC27A547485195902293259023364

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr19:59010865-59010865p.T554I4
chr19:59012030-59012030p.N409T3
chr19:59010864-59010864p.T554T3
chr19:59012675-59012675p.R387Q2
chr19:59022888-59022888p.F145F2
chr19:59010893-59010893p.L545V2
chr19:59023004-59023004p.C107G2
chr19:59010864-59010865p.T554I2
chr19:59022196-59022196p.L264M2
chr19:59023174-59023174p.M50T2

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample43 9  3 3  462  136 5
# mutation43 9  4 3  462  118 5
nonsynonymous SNV32 8  2 2  241  45 3
synonymous SNV11 1  2 1  221  73 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr19:59010864p.T554T4
chr19:59010865p.R550C2
chr19:59010878p.T554I2
chr19:59012663p.N391S1
chr19:59021320p.L264L1
chr19:59010492p.R387Q1
chr19:59022708p.A263V1
chr19:59011880p.V529F1
chr19:59012675p.L386L1
chr19:59021339p.G260E1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00145solute carrier family 27 (fatty acid transporter), member 5approved; nutraceuticalGlycine


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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



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