Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 LRAT

Basic gene info.	Gene symbol	LRAT
	Gene name	lecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase)
	Synonyms	LCA14
	Cytomap	UCSC genome browser: 4q32.1
	Genomic location	chr4 :155665162-155674270
	Type of gene	protein-coding
	RefGenes	NM_001301645.1, NM_004744.4,
	Ensembl id	ENSG00000121207
	Description	lecithin retinol acyltransferase
	Modification date	20141219
dbXrefs	MIM : 604863
	HGNC : HGNC
	Ensembl : ENSG00000121207
	HPRD : 05332
	Vega : OTTHUMG00000161418
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_LRAT
	BioGPS: 9227
	Gene Expression Atlas: ENSG00000121207
	The Human Protein Atlas: ENSG00000121207
Pathway	NCI Pathway Interaction Database: LRAT
	KEGG: LRAT
	REACTOME: LRAT
	ConsensusPathDB
	Pathway Commons: LRAT
Metabolism	MetaCyc: LRAT
	HUMANCyc: LRAT
Regulation	Ensembl's Regulation: ENSG00000121207
	miRBase: chr4 :155,665,162-155,674,270
	TargetScan: NM_001301645
	cisRED: ENSG00000121207
Context	iHOP: LRAT
	cancer metabolism search in PubMed: LRAT
	UCL Cancer Institute: LRAT
Assigned class in ccmGDB	C

Top

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

Cancer Description
Cancer	CGAP: LRAT
	Familial Cancer Database: LRAT

* 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_RETINOL_METABOLISM REACTOME_METABOLISM_OF_STEROID_HORMONES_AND_VITAMINS_A_AND_D REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

Mutations for LRAT

* 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 LRAT 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

BX093249

AVL9

168

32800309

32800442

LRAT

165

748

155672877

155673456

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

There's no copy number variation information in COSMIC data for this gene.

Top

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=3

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=23)	Stat. for Synonymous SNVs (# total SNVs=6)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

Top

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
chr4:155665867-155665867	p.S130F	3
chr4:155665742-155665742	p.T88T	2
chr4:155665779-155665779	p.V101I	2
chr4:155666013-155666013	p.D179Y	2
chr4:155670163-155670163	p.R190C	2
chr4:155665896-155665896	p.E140K	1
chr4:155665550-155665550	p.L24L	1
chr4:155670221-155670221	p.T209M	1
chr4:155665754-155665754	p.V92V	1
chr4:155665906-155665906	p.R143Q	1

Top

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	1		4	1		5		1			6	2				3	5		6
# mutation	1	1		4	1		5		1			6	2				3	5		6
nonsynonymous SNV				3	1		5		1			4	2				3	3		4
synonymous SNV	1	1		1								2						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])

Top

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
chr4:155665738	p.R87L	2
chr4:155670222	p.T209T	2
chr4:155665906	p.R69S	1
chr4:155665582	p.E140K	1
chr4:155670262	p.R143Q	1
chr4:155665742	p.R69H	1
chr4:155665918	p.K147R	1
chr4:155665617	p.A71A	1
chr4:155670267	p.D179H	1
chr4:155665754	p.M73I	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 LRAT 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]

Top

Gene Expression for LRAT

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


BNC1,C11orf87,CDH4,CSRP2,FGFBP1,FSCN1,GJB3, GJB5,HAS3,HSD17B3,KRT5,KRT6B,KRT75,LRAT, MYO7B,OR2J3,PCSK9,PLEK2,RPSAP52,S100A2,SOX15	MGME1,FAXC,TDRP,CHMP4C,FAM60A,FGFR2,GRAMD3, GRHL1,KIAA1804,LRAT,MCTP2,NEBL,NSUN7,PRSS16, REPS1,ZBED9,SDR42E1,SUDS3,TFAP2C,VANGL2,ZNF140

ACTBL2,ANXA8,ANXA8L1,BPI,C8orf86,CGB1,CPA4, CST6,FAM3C,IL20RB,KRT7,LIPK,LRAT,MUC16, MYH16,PEX5L,PSG6,PSG9,SIGLEC15,THEG,WNT7A	APOB,CPO,CPS1,CUBN,DAB1,DFNA5,ENPEP, FMO1,KCNJ13,KHK,LOC285733,LRAT,MTTP,OAT, PDZD7,SEC14L2,SLC28A1,SLC5A4,SOAT2,TMPRSS15,UGT3A1

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for LRAT

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
DB00162	lecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase)	approved; nutraceutical	Vitamin A

Top

Cross referenced IDs for LRAT

* 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