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 LRAT
Basic gene info.Gene symbolLRAT
Gene namelecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase)
SynonymsLCA14
CytomapUCSC genome browser: 4q32.1
Genomic locationchr4 :155665162-155674270
Type of geneprotein-coding
RefGenesNM_001301645.1,
NM_004744.4,
Ensembl idENSG00000121207
Descriptionlecithin retinol acyltransferase
Modification date20141219
dbXrefs MIM : 604863
HGNC : HGNC
Ensembl : ENSG00000121207
HPRD : 05332
Vega : OTTHUMG00000161418
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LRAT
BioGPS: 9227
Gene Expression Atlas: ENSG00000121207
The Human Protein Atlas: ENSG00000121207
PathwayNCI Pathway Interaction Database: LRAT
KEGG: LRAT
REACTOME: LRAT
ConsensusPathDB
Pathway Commons: LRAT
MetabolismMetaCyc: LRAT
HUMANCyc: LRAT
RegulationEnsembl's Regulation: ENSG00000121207
miRBase: chr4 :155,665,162-155,674,270
TargetScan: NM_001301645
cisRED: ENSG00000121207
ContextiHOP: LRAT
cancer metabolism search in PubMed: LRAT
UCL Cancer Institute: LRAT
Assigned class in ccmGDBC

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

check002.gifMetabolic Pathway Description
KEGG_RETINOL_METABOLISM
REACTOME_METABOLISM_OF_STEROID_HORMONES_AND_VITAMINS_A_AND_D
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LRAT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BX093249AVL93516873280030932800442LRAT1657484155672877155673456

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=3

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check002.gifSomatic 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.

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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
chr4:155665867-155665867p.S130F3
chr4:155665779-155665779p.V101I2
chr4:155666013-155666013p.D179Y2
chr4:155670163-155670163p.R190C2
chr4:155665742-155665742p.T88T2
chr4:155665965-155665965p.H163Y1
chr4:155665684-155665684p.R69H1
chr4:155670267-155670267p.F224L1
chr4:155665803-155665803p.R109C1
chr4:155665691-155665691p.A71A1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 41 5 1  62   35 6
# mutation11 41 5 1  62   35 6
nonsynonymous SNV   31 5 1  42   33 4
synonymous SNV11 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])

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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
chr4:155670222p.R87L2
chr4:155665738p.T209T2
chr4:155665633p.R55W1
chr4:155665764p.N138N1
chr4:155670149p.R69S1
chr4:155665641p.E140K1
chr4:155665772p.R69H1
chr4:155670163p.R143Q1
chr4:155665683p.A71A1
chr4:155665779p.K147R1

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 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]

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Gene Expression for LRAT

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

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
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 LRAT
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
DB00162lecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase)approved; nutraceuticalVitamin A


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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



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