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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for APOE |
 Gene summary |
| Gene information | Gene symbol | APOE | Gene ID | 348 |
| Gene name | apolipoprotein E | |
| Synonyms | AD2|APO-E|ApoE4|LDLCQ5|LPG | |
| Cytomap | 19q13.32 | |
| Type of gene | protein-coding | |
| Description | apolipoprotein Eapolipoprotein E3 | |
| Modification date | 20200329 | |
| UniProtAcc | ||
| Context | - 28434655(Apolipoprotein E, Receptors, and Modulation of Alzheimer's Disease) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| APOE | GO:0001937 | negative regulation of endothelial cell proliferation | 9685360 |
| APOE | GO:0006641 | triglyceride metabolic process | 9649566 |
| APOE | GO:0006898 | receptor-mediated endocytosis | 1917954 |
| APOE | GO:0007186 | G protein-coupled receptor signaling pathway | 16443932 |
| APOE | GO:0007263 | nitric oxide mediated signal transduction | 8995232 |
| APOE | GO:0008203 | cholesterol metabolic process | 9649566 |
| APOE | GO:0010544 | negative regulation of platelet activation | 8995232 |
| APOE | GO:0010873 | positive regulation of cholesterol esterification | 15654758 |
| APOE | GO:0010875 | positive regulation of cholesterol efflux | 12042316|14754908 |
| APOE | GO:0010976 | positive regulation of neuron projection development | 7592957|23845000 |
| APOE | GO:0010977 | negative regulation of neuron projection development | 7592957 |
| APOE | GO:0015909 | long-chain fatty acid transport | 24345162 |
| APOE | GO:0017038 | protein import | 24446231 |
| APOE | GO:0019934 | cGMP-mediated signaling | 8995232 |
| APOE | GO:0030195 | negative regulation of blood coagulation | 8995232 |
| APOE | GO:0031175 | neuron projection development | 8939961 |
| APOE | GO:0032489 | regulation of Cdc42 protein signal transduction | 16443932 |
| APOE | GO:0032805 | positive regulation of low-density lipoprotein particle receptor catabolic process | 15950758 |
| APOE | GO:0033344 | cholesterol efflux | 11162594|16443932|23620513 |
| APOE | GO:0033700 | phospholipid efflux | 11162594 |
| APOE | GO:0034372 | very-low-density lipoprotein particle remodeling | 15654758 |
| APOE | GO:0034380 | high-density lipoprotein particle assembly | 14754908|17305370 |
| APOE | GO:0034382 | chylomicron remnant clearance | 1911868 |
| APOE | GO:0034384 | high-density lipoprotein particle clearance | 210175 |
| APOE | GO:0034447 | very-low-density lipoprotein particle clearance | 1917954|2762297 |
| APOE | GO:0042158 | lipoprotein biosynthetic process | 23620513 |
| APOE | GO:0042632 | cholesterol homeostasis | 9649566 |
| APOE | GO:0042982 | amyloid precursor protein metabolic process | 21593558 |
| APOE | GO:0043254 | regulation of protein complex assembly | 25207746 |
| APOE | GO:0043407 | negative regulation of MAP kinase activity | 9685360 |
| APOE | GO:0043537 | negative regulation of blood vessel endothelial cell migration | 9685360 |
| APOE | GO:0043691 | reverse cholesterol transport | 8127890 |
| APOE | GO:0045541 | negative regulation of cholesterol biosynthetic process | 1917954 |
| APOE | GO:0045807 | positive regulation of endocytosis | 7683668|8300609 |
| APOE | GO:0046889 | positive regulation of lipid biosynthetic process | 12042316 |
| APOE | GO:0051000 | positive regulation of nitric-oxide synthase activity | 8995232 |
| APOE | GO:0051044 | positive regulation of membrane protein ectodomain proteolysis | 15950758 |
| APOE | GO:0055089 | fatty acid homeostasis | 24345162 |
| APOE | GO:0060999 | positive regulation of dendritic spine development | 24328732 |
| APOE | GO:0071831 | intermediate-density lipoprotein particle clearance | 1917954 |
| APOE | GO:0090090 | negative regulation of canonical Wnt signaling pathway | 16805831 |
| APOE | GO:0097113 | AMPA glutamate receptor clustering | 24328732 |
| APOE | GO:0097114 | NMDA glutamate receptor clustering | 24328732 |
| APOE | GO:1900221 | regulation of amyloid-beta clearance | 24446231 |
| APOE | GO:1900272 | negative regulation of long-term synaptic potentiation | 16273551 |
| APOE | GO:1902430 | negative regulation of amyloid-beta formation | 24154541 |
| APOE | GO:1902952 | positive regulation of dendritic spine maintenance | 24328732 |
| APOE | GO:1902991 | regulation of amyloid precursor protein catabolic process | 28164773 |
| APOE | GO:1902995 | positive regulation of phospholipid efflux | 12042316 |
| APOE | GO:1903002 | positive regulation of lipid transport across blood brain barrier | 24345162 |
| APOE | GO:1905855 | positive regulation of heparan sulfate binding | 7683668 |
| APOE | GO:1905860 | positive regulation of heparan sulfate proteoglycan binding | 8300609 |
| APOE | GO:1905890 | regulation of cellular response to very-low-density lipoprotein particle stimulus | 7592957 |
| APOE | GO:1905906 | regulation of amyloid fibril formation | 25207746 |
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Gene structures and expression levels for APOE |
| Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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ENSG00000130203
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for APOE |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_105353 | chr19 | 44906602:44906667:44907760:44907952:44908533:44908602 | 44907760:44907952 |
| exon_skip_147425 | chr19 | 44905796:44905841:44906602:44906667:44907760:44907843 | 44906602:44906667 |
| exon_skip_160787 | chr19 | 44905796:44905841:44906602:44906667:44907760:44907952 | 44906602:44906667 |
| exon_skip_273935 | chr19 | 44905796:44905841:44906602:44906667:44907760:44907949 | 44906602:44906667 |
| exon_skip_283722 | chr19 | 44906602:44906667:44907760:44907952:44908533:44908631 | 44907760:44907952 |
| exon_skip_53012 | chr19 | 44905796:44905841:44906602:44906667:44907760:44907951 | 44906602:44906667 |
| exon_skip_55098 | chr19 | 44905796:44905841:44906602:44906667:44907760:44907881 | 44906602:44906667 |
| exon_skip_58375 | chr19 | 44906602:44906667:44907760:44907952:44908533:44908545 | 44907760:44907952 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for APOE |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000252486 | 44906602 | 44906667 | 5CDS-5UTR |
| ENST00000252486 | 44907760 | 44907952 | Frame-shift |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000252486 | 44906602 | 44906667 | 5CDS-5UTR |
| ENST00000252486 | 44907760 | 44907952 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for APOE |
p-ENSG00000130203_img4.png |
| Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Lost protein functional features of individual exon skipping events in MSBB. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Lost protein functional features of individual exon skipping events in Mayo. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
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3'-UTR located exon skipping events that lost miRNA binding sites in APOE |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for APOE |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for APOE |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for APOE |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for APOE |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for APOE |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| P02649 | approved|investigational | DB01593 | Zinc | small molecule | P02649 |
| P02649 | approved|investigational | DB14487 | Zinc acetate | small molecule | P02649 |
| P02649 | approved|investigational | DB14533 | Zinc chloride | small molecule | P02649 |
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RelatedDiseases for APOE |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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