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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for LCAT
check button Gene summary
Basic gene informationGene symbolLCAT
Gene namelecithin-cholesterol acyltransferase
Synonyms-
CytomapUCSC genome browser: 16q22.1
Type of geneprotein-coding
RefGenesNM_000229.1,
Descriptionphosphatidylcholine-sterol acyltransferasephospholipid-cholesterol acyltransferase
Modification date20141207
dbXrefs MIM : 606967
HGNC : HGNC
Ensembl : ENSG00000213398
HPRD : 06098
Vega : OTTHUMG00000137551
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LCAT
BioGPS: 3931
PathwayNCI Pathway Interaction Database: LCAT
KEGG: LCAT
REACTOME: LCAT
Pathway Commons: LCAT
ContextiHOP: LCAT
ligand binding site mutation search in PubMed: LCAT
UCL Cancer Institute: LCAT
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)LiverProstate
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LIHCPRAD
Reference showing the relevant tissue of LCAT
Description by TissGene annotations
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID
GO:0006644phospholipid metabolic process4335615
GO:0006656phosphatidylcholine biosynthetic process11966470
GO:0008203cholesterol metabolic process10559507
GO:0030301cholesterol transport10559507
GO:0034372very-low-density lipoprotein particle remodeling15654758
GO:0034375high-density lipoprotein particle remodeling10722751
GO:0034435cholesterol esterification3458198
GO:0042632cholesterol homeostasis4335615
GO:0043691reverse cholesterol transport4335615
GO:0006644phospholipid metabolic process4335615
GO:0006656phosphatidylcholine biosynthetic process11966470
GO:0008203cholesterol metabolic process10559507
GO:0030301cholesterol transport10559507
GO:0034372very-low-density lipoprotein particle remodeling15654758
GO:0034375high-density lipoprotein particle remodeling10722751
GO:0034435cholesterol esterification3458198
GO:0042632cholesterol homeostasis4335615
GO:0043691reverse cholesterol transport4335615


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TissGeneExp for LCAT

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
LIHC1.7773573095.464339309-3.6869821.81E-178.74E-16
BRCA-2.116815778-0.40491841-1.7118973687.06E-453.06E-43
LUSC-1.4326738280.082122251-1.5147960782.81E-151.81E-14
LUAD-1.36129276-0.119653104-1.2416396551.61E-131.38E-12


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TissGene-miRNA for LCAT

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for LCAT
TissGeneSNV for LCAT

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
* Click on the image to enlarge it in a new window.
SNV lollipop
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.S132YKIRP1
p.S138GSTAD1
p.P278SCESC1
p.Q220HUCEC1
p.D101NCOAD1
p.I269KKICH1
p.L324IREAD1
p.V49IUCEC1
p.R47QUCEC1
p.E179DLUAD1
p.G332DSTAD1
p.T12PLIHC1
p.E178KESCA1
p.F32IBRCA1
p.G239VLIHC1
p.S279CHNSC1
p.D301NLUAD1
p.P344LLIHC1
p.R280HUCEC1
p.R182HSTAD1
p.E179*LUAD1
p.S249LBLCA1
p.A282VUCEC1
p.V288MSTAD1
p.P256SCESC1
p.R164CSTAD1
p.I231MLUAD1
p.A117TGBM1
p.G239VKIRP1
p.D367HCESC1
p.F230SPRAD1
p.A330VCOAD1


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TissGeneCNV for LCAT

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for LCAT

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0ChiTaRsNAX06537RPL13A-LCATchr19:49995310chr16:67973786


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TissGeneNet for LCAT

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)
BRCA (tumor)BRCA (normal)
LCAT, SP1, SP3, A2M, APOA1 (tumor)LCAT, SP1, SP3, A2M, APOA1 (normal)
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COAD (tumor)COAD (normal)
LCAT, SP1, SP3, A2M, APOA1 (tumor)LCAT, SP1, SP3, A2M, APOA1 (normal)
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HNSC (tumor)HNSC (normal)
LCAT, SP1, SP3, A2M, APOA1 (tumor)LCAT, SP1, SP3, A2M, APOA1 (normal)
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KICH (tumor)KICH (normal)
LCAT, SP1, SP3, A2M, APOA1 (tumor)LCAT, SP1, SP3, A2M, APOA1 (normal)
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KIRC (tumor)KIRC (normal)
LCAT, SP1, SP3, A2M, APOA1 (tumor)LCAT, SP1, SP3, A2M, APOA1 (normal)
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KIRP (tumor)KIRP (normal)
LCAT, SP1, SP3, A2M, APOA1 (tumor)LCAT, SP1, SP3, A2M, APOA1 (normal)
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LIHC (tumor)LIHC (normal)
LCAT, SP1, SP3, A2M, APOA1 (tumor)LCAT, SP1, SP3, A2M, APOA1 (normal)
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LUAD (tumor)LUAD (normal)
LCAT, SP1, SP3, A2M, APOA1 (tumor)LCAT, SP1, SP3, A2M, APOA1 (normal)
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LUSC (tumor)LUSC (normal)
LCAT, SP1, SP3, A2M, APOA1 (tumor)LCAT, SP1, SP3, A2M, APOA1 (normal)
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PRAD (tumor)PRAD (normal)
LCAT, SP1, SP3, A2M, APOA1 (tumor)LCAT, SP1, SP3, A2M, APOA1 (normal)
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STAD (tumor)STAD (normal)
LCAT, SP1, SP3, A2M, APOA1 (tumor)LCAT, SP1, SP3, A2M, APOA1 (normal)
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THCA (tumor)THCA (normal)
LCAT, SP1, SP3, A2M, APOA1 (tumor)LCAT, SP1, SP3, A2M, APOA1 (normal)
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TissGeneProg for LCAT

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for LCAT
TissGeneDrug for LCAT

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status


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TissGeneDisease for LCAT

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0023195Lecithin Acyltransferase Deficiency36BeFree,CLINVAR,CTD_human,GAD,LHGDN,MGD,ORPHANET,UNIPROT
umls:C0342895Fish-Eye Disease21BeFree,CLINVAR,GAD,MGD,ORPHANET,UNIPROT
umls:C0004153Atherosclerosis14BeFree,GAD,LHGDN
umls:C0003850Arteriosclerosis11BeFree
umls:C0242339Dyslipidemias4BeFree,GAD
umls:C0010054Coronary Arteriosclerosis3BeFree,GAD
umls:C0010068Coronary heart disease3BeFree,GAD
umls:C0011860Diabetes Mellitus, Non-Insulin-Dependent3GAD
umls:C0020473Hyperlipidemia3GAD,LHGDN,RGD
umls:C0022661Kidney Failure, Chronic3BeFree,RGD
umls:C0035078Kidney Failure3BeFree
umls:C1956346Coronary Artery Disease3BeFree,LHGDN
umls:C0007222Cardiovascular Diseases2BeFree
umls:C0022658Kidney Diseases2BeFree
umls:C0023817Hyperlipoproteinemia Type I2BeFree
umls:C0028754Obesity2BeFree
umls:C0154251Lipid Metabolism Disorders2BeFree,GAD
umls:C0342883Cholesteryl Ester Transfer Protein Deficiency2BeFree
umls:C0473527Hypoalphalipoproteinemias2GAD
umls:C1704429Hypoalphalipoproteinemia, Familial2BeFree
umls:C0002395Alzheimer's Disease1GAD
umls:C0005684Malignant neoplasm of urinary bladder1GAD
umls:C0007785Cerebral Infarction1LHGDN
umls:C0020476Hyperlipoproteinemias1BeFree
umls:C0020557Hypertriglyceridemia1GAD
umls:C0021368Inflammation1GAD
umls:C0021655Insulin Resistance1GAD
umls:C0023895Liver diseases1BeFree
umls:C0024117Chronic Obstructive Airway Disease1GAD
umls:C0025521Inborn Errors of Metabolism1BeFree
umls:C0027051Myocardial Infarction1RGD
umls:C0155733Atherosclerosis of aorta1BeFree
umls:C0242379Malignant neoplasm of lung1GAD
umls:C0497327Dementia1GAD
umls:C1522137Hypertriglyceridemia result1GAD
umls:C3711531Hdl Deficiency, Type 21BeFree