EDK
Editome Disease Knowledgebase
FAQ
1. Introduction
Editome Disease Knowledgebase (EDK), is a curated knowledgebase of RNA editome-disease associations. Unlike extant relevant data-oriented databases, EDK features comprehensive integration of knowledge on abnormal RNA editing events and aberrant RNA editing enzyme activities, which are associated with human diseases. Therefore, EDK would be of great help to provide a landscape of editome-disease associations and to explore the RNA editing machineries underlying different human diseases.
2. Datasets
The current version of EDK incorporates 65 diseases (grouped into 10 categories) associated with 248 experimentally validated aberrant editing events that occur in 32 mRNAs, 16 miRNAs, 1 lncRNA and 11 viruses, as well as 44 aberrant activities involved with 6 editing enzymes, which are all manually curated from over 200 publications.
3. Statistics
4. Data Structure
5. Classification of disease
In the current implementation, EDK integrates 65 editome-associated diseases, including 27 cancers (42%), 15 nervous system diseases (23%), 6 viral infectious diseases (9%), 4 gastrointestinal system diseases (6%), 2 cognitive disorders (3%), 2 diseases of metabolism (3%), 2 genetic diseases (3%), 2 cardiovascular system disease (3%), 2 skin disease (3%), and 3 other types (5%).
6. Annotation
- Gene Annotation
- miRNA Annotation
For each gene, the mRNA information from NCBI-gene, the associated transcripts from NCBI-Nucleotide, together with the protein information from Uniprot, GTEx and Genecard are offered.
For each miRNA, the associated stem-loop sequence and mature sequence from miRBase are provided in the miRNA function.
7. Controlled Vocabularies
| Data type | Description | Value |
|---|---|---|
| Enzyme | Controlled vocabulary | ADAR1, ADAR2, ADAR3, AID, APOBEC1, APOBEC3 |
| Editing Type | Controlled vocabulary | Substitution(A-to-I, G-to-A, C-to-U, U-to-C, G-to-C), Insertion, Deletion |
| Editing Region | Controlled vocabulary | CDS, Exonic, Intronic, Downstream, 5’UTR, 3’UTR |
| Molecular Consequence | Controlled vocabulary | Nonsynonymous substitution; mRNA expression change; mRNA stability change; Alternative splicing… |
| Editing Level | Controlled vocabulary | Increased; Decreased; Present; Absent |
| Relationship | Controlled vocabulary | Causative; Correlated |
| Correlation | Controlled vocabulary | Positive; Negative |
| Editing Effect | The regulation mechanism of RNA editing affecting disease | eg:RNA-editing in the CTSS 3'UTR can knockdown the CTSS mRNA expression and deficiency of cathepsin S reduces atherosclerosis and angiogenesis in vivo. |
| Phenotype | The influence of editing on disease | Promote the disease risk; Promote tumor cell proliferation… |
| Description | This item describes in detail how the RNA editing event acts on genes and influences disease | eg: RNA-editing in the CTSS 3'UTR will knockdown the CTSS mRNA expression; and RNA-editing of CTSS mRNA also regulates the RNA-binding protein HuR; deficiency of cathepsin S reduces atherosclerosis and angiogenesis in vivo. And it will reduce the binding efficiency of HuR; which will leads to decrease the stability of CTSS mRNA. |
| Disease | Disease associated with RNA editing | Atherosclerosis; Alzheimer's Disease; Hepatocellular Carcinoma… |
| Target Change(miRNA) | The edited miRNA may change its target gene | PCDH9->ADAM12; Rab15->Rab15; CPEB1->CPEB1… |
| Regulation Target(miRNA) | The changes of target gene or target gene expression regulated by edited miRNA | Retarget ADAM12 replaces original target PCDH9; Increase Rab15 expression; Inhibit ZEB1 expression… |
| Target(lncRNA) | lncRNA target | PRUNE2 |
| Edited gene(virus) | The edited virus gene | Phosphoprotein gene; Glycoprotein gene… |
| Virus Protein(virus) | Protein composition of the virus | M,R,D,V,P,V,I,S,R,Y,Y; N,P/C,M,F,H,N,L… |
| Regulator(enzyme) | Protein or interferon regulate the expression or mutation of enzyme | JAK2; IFN… |
| Expression/Aberrance(enzyme) | Mutation or expression change of enzyme | Mutation; Expression Increase… |
| Target(enzyme) | The aberrant enzyme can affect the RNA editing of target molecular | AZIN1; STAT1; miR-222; virus HBV… |
8. Ontologies
- Disease Ontology
- Tissue Ontology
To unify disease name and definition, terms or identifiers of Disease Ontology (DO), Experimental Factor Ontology (EFO), Online Mendelian Inheritance in Man (OMIM) and National Cancer Institute (NCI) were retrieved and mapped to the corresponding diseases.
The reported tissues were mapped to terms from the Experimental Factor Ontology (EFO)
9. External Links