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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 APOC1
check button Gene summary
Basic gene informationGene symbolAPOC1
Gene nameapolipoprotein C-I
SynonymsApo-CI|ApoC-I
CytomapUCSC genome browser: 19q13.2
Type of geneprotein-coding
RefGenesNM_001645.3,
Descriptionapo-CIBapoC-IBapolipoprotein C-I variant Iapolipoprotein C1
Modification date20141211
dbXrefs MIM : 107710
HGNC : HGNC
Ensembl : ENSG00000130208
HPRD : 00131
Vega : OTTHUMG00000180844
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_APOC1
BioGPS: 341
PathwayNCI Pathway Interaction Database: APOC1
KEGG: APOC1
REACTOME: APOC1
Pathway Commons: APOC1
ContextiHOP: APOC1
ligand binding site mutation search in PubMed: APOC1
UCL Cancer Institute: APOC1
Assigned class in TissGDB*A
Included tissue-specific gene expression resourcesHPA,TiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Liver
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LIHC
Reference showing the relevant tissue of APOC1Hyperlipidemia and cutaneous abnormalities in transgenic mice overexpressing human apolipoprotein C1. Jong MC, Gijbels MJ, Dahlmans VE, Gorp PJ, Koopman SJ, Ponec M, Hofker MH, Havekes LM. J Clin Invest. 1998 Jan 1;101(1):145-52. (pmid:9421476)
go to article
Description by TissGene annotationsCancer gene
Fused withTSGene
* 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:0010900negative regulation of phosphatidylcholine catabolic process2302419
GO:0010916negative regulation of very-low-density lipoprotein particle clearance1917954
GO:0032375negative regulation of cholesterol transport10978346
GO:0033344cholesterol efflux11162594
GO:0033700phospholipid efflux11162594
GO:0034369plasma lipoprotein particle remodeling10978346
GO:0034382chylomicron remnant clearance4020294
GO:0045717negative regulation of fatty acid biosynthetic process15576844
GO:0045833negative regulation of lipid metabolic process182536
GO:0048261negative regulation of receptor-mediated endocytosis1917954
GO:0050995negative regulation of lipid catabolic process15576844
GO:0051005negative regulation of lipoprotein lipase activity15576844
GO:0010900negative regulation of phosphatidylcholine catabolic process2302419
GO:0010916negative regulation of very-low-density lipoprotein particle clearance1917954
GO:0032375negative regulation of cholesterol transport10978346
GO:0033344cholesterol efflux11162594
GO:0033700phospholipid efflux11162594
GO:0034369plasma lipoprotein particle remodeling10978346
GO:0034382chylomicron remnant clearance4020294
GO:0045717negative regulation of fatty acid biosynthetic process15576844
GO:0045833negative regulation of lipid metabolic process182536
GO:0048261negative regulation of receptor-mediated endocytosis1917954
GO:0050995negative regulation of lipid catabolic process15576844
GO:0051005negative regulation of lipoprotein lipase activity15576844


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TissGeneExp for APOC1

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
LUAD1.9372152773.698906657-1.7616913791.47E-108.59E-10
PRAD-0.681470465-2.4412570041.7597865386.00E-097.82E-08
KIRP2.342420881-3.3280791195.67051.38E-187.02E-17
KIRC2.051465325-3.4843138415.5357791671.31E-415.99E-40
KICH0.156488381-3.4472196193.6037085.66E-114.61E-10
LUSC1.1797377933.451863283-2.272125497.67E-123.24E-11
THCA1.545598211-0.6199136532.1655118642.77E-081.30E-07
STAD0.091414631-3.6551134943.7465281251.76E-091.28E-07
ESCA-1.675918892-4.1866734372.5107545450.0006180.010412364
BLCA0.396108381-1.6916810932.0877894740.001040.00734273
COAD0.086185304-1.1894031581.2755884620.002020.005437125
HNSC-0.713484642-2.4024637121.688979070.000210.00085443
LIHC7.7058083818.885142381-1.1793340.0002260.000717066


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TissGene-miRNA for APOC1

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 APOC1
TissGeneSNV for APOC1

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.K38RLUAD1
p.E77KSKCM1
p.M1IBLCA1
p.I52MHNSC1
p.S69PUCEC1
p.R65LLUAD1
p.K38NPRAD1
p.R54HUCEC1
p.V75AUCEC1
p.R49WSKCM1


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TissGeneCNV for APOC1

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 APOC1

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
Chimerdb3.0ChiTaRsNABP389649HIVEP3-APOC1chr1:42216188chr19:45419445
Chimerdb3.0ChiTaRsNADA183106APOC1-LAMA1chr19:45419584chr18:7040169
TCGAfusionPortalPRADALUADTCGA-86-A4P7-01AAPOC1-IQCE3UTR-CDSChr19:45422606Chr7:2641075


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TissGeneNet for APOC1

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)
APOC1, ALB, APOA1, APOA2 (tumor)APOC1, ALB, APOA1, APOA2 (normal)
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COAD (tumor)COAD (normal)
APOC1, ALB, APOA1, APOA2 (tumor)APOC1, ALB, APOA1, APOA2 (normal)
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HNSC (tumor)HNSC (normal)
APOC1, ALB, APOA1, APOA2 (tumor)APOC1, ALB, APOA1, APOA2 (normal)
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KICH (tumor)KICH (normal)
APOC1, ALB, APOA1, APOA2 (tumor)APOC1, ALB, APOA1, APOA2 (normal)
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KIRC (tumor)KIRC (normal)
APOC1, ALB, APOA1, APOA2 (tumor)APOC1, ALB, APOA1, APOA2 (normal)
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KIRP (tumor)KIRP (normal)
APOC1, ALB, APOA1, APOA2 (tumor)APOC1, ALB, APOA1, APOA2 (normal)
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LIHC (tumor)LIHC (normal)
APOC1, ALB, APOA1, APOA2 (tumor)APOC1, ALB, APOA1, APOA2 (normal)
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LUAD (tumor)LUAD (normal)
APOC1, ALB, APOA1, APOA2 (tumor)APOC1, ALB, APOA1, APOA2 (normal)
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LUSC (tumor)LUSC (normal)
APOC1, ALB, APOA1, APOA2 (tumor)APOC1, ALB, APOA1, APOA2 (normal)
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PRAD (tumor)PRAD (normal)
APOC1, ALB, APOA1, APOA2 (tumor)APOC1, ALB, APOA1, APOA2 (normal)
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STAD (tumor)STAD (normal)
APOC1, ALB, APOA1, APOA2 (tumor)APOC1, ALB, APOA1, APOA2 (normal)
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THCA (tumor)THCA (normal)
APOC1, ALB, APOA1, APOA2 (tumor)APOC1, ALB, APOA1, APOA2 (normal)
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TissGeneProg for APOC1

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 APOC1
TissGeneDrug for APOC1

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 APOC1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0002395Alzheimer's Disease15BeFree,GAD,GWASCAT,LHGDN
umls:C0010068Coronary heart disease7BeFree,GAD,LHGDN
umls:C1956346Coronary Artery Disease6BeFree,GAD
umls:C0007222Cardiovascular Diseases5BeFree,GAD,GWASCAT
umls:C0020473Hyperlipidemia5BeFree
umls:C0010054Coronary Arteriosclerosis4BeFree,GAD
umls:C0028754Obesity4BeFree,GAD
umls:C0011265Presenile dementia3BeFree
umls:C0338656Impaired cognition3BeFree,GAD,GWASCAT
umls:C0497327Dementia3BeFree
umls:C0524620Metabolic Syndrome X3BeFree
umls:C0011860Diabetes Mellitus, Non-Insulin-Dependent2GAD
umls:C0019196Hepatitis C2GAD,LHGDN
umls:C0027126Myotonic Dystrophy2BeFree
umls:C0037268Skin Abnormalities2BeFree
umls:C0233794Memory impairment2BeFree,GAD
umls:C0338657Age-associated memory impairment2BeFree,GAD
umls:C0410226Congenital Myotonic Dystrophy2BeFree
umls:C0004153Atherosclerosis1LHGDN
umls:C0007134Renal Cell Carcinoma1GAD
umls:C0008350Cholelithiasis1BeFree,GAD
umls:C0009241Cognition Disorders1GAD
umls:C0011615Dermatitis, Atopic1BeFree,LHGDN
umls:C0011854Diabetes Mellitus, Insulin-Dependent1GAD
umls:C0011881Diabetic Nephropathy1GAD
umls:C0013595Eczema1BeFree
umls:C0015695Fatty Liver1BeFree
umls:C0017661IGA Glomerulonephritis1CTD_human
umls:C0020459Hyperinsulinism1BeFree
umls:C0020479Hyperlipoproteinemia Type III1BeFree,GAD
umls:C0020538Hypertensive disease1BeFree
umls:C0021368Inflammation1GAD
umls:C0022665Kidney Neoplasm1GAD
umls:C0023462Acute Megakaryocytic Leukemias1BeFree
umls:C0026769Multiple Sclerosis1GAD
umls:C0030297Pancreatic Neoplasm1LHGDN
umls:C0151514Atrophic condition of skin1BeFree
umls:C0205645Adenocarcinoma, Tubular1BeFree
umls:C0234985Mental deterioration1GWASCAT
umls:C0235974Pancreatic carcinoma1BeFree
umls:C0236642Pick Disease of the Brain1BeFree
umls:C0242216Biliary calculi1LHGDN
umls:C0242383Age related macular degeneration1GWASCAT
umls:C0243026Sepsis1LHGDN
umls:C0263641Epithelial hyperplasia of skin1BeFree
umls:C0282513Primary Progressive Aphasia (disorder)1BeFree
umls:C0338451Frontotemporal dementia1BeFree
umls:C0346647Malignant neoplasm of pancreas1BeFree
umls:C0423773Scaly skin1BeFree
umls:C0494463Alzheimer Disease, Late Onset1BeFree
umls:C0870082Hyperkeratosis1BeFree
umls:C0947622Cholecystolithiasis1GAD
umls:C1134719Invasive Ductal Breast Carcinoma1BeFree
umls:C1335302Pancreatic Ductal Adenocarcinoma1BeFree
umls:C1335475Primary Carcinoma1BeFree
umls:C2711227Steatohepatitis1BeFree
umls:C2712907Combined hyperlipidemia1BeFree
umls:C3714514Infection1LHGDN
umls:C3714619Insulin resistance syndrome1BeFree