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1. RNA A-to-I editing information for ROSMAP, MSBB, and Mayo2. Understanding annotation of ADeditome
Search page, example: SERPINA3
Gene search result page
Gene annotation result page
1) Gene summary
2) RNA A-to-I events
3) RNA A-to-I editing positional annotations
4) RNA A-to-I editing events in the alternative splicing sites
5) Differntial gene expression between RNA A-to-I edited versus non-edited samples
6) Protein coding region RNA A-to-I editings
7) The effects of the RNA editing to the miRNA binding sites
8) The effects of the RNA editing to the stability of the RNA structures
9) Relation with ADAR
10) Relation with AD stages
11) Related drugs and diseases with this gene
3. Download data and contact us
1. Identifying RNA A-to-I editing events ROSMAP, MSBB, and Mayo
We downloaded RNA-Seq bam files and clinical information of three cohorts from the AMP-AD Knowledge Portal. According to the diagnosis annotations of each cohort, we chose AD and control samples per tissue type. We re-mapped RNA-seq bam files to GRCh38 using STAR. To predict RNA-editing events, we applied an approach REDItools (high-throughput RNA editing detection made easy). Specifically, we focused on known editing sites, which were downloaded from REDIportal and lifted over GRCh37 to GRCh38. To rule out DNA changes that may affect the detection of RNA editing events, the germline single nucleotide polymorphisms (SNP) were excluded. Then we ran REDItools with default setting (e.g., minimal read coverage, 10; minimal quality score, 30; and minimal mapping quality score, 255). Since the A-to-I RNA editing is the major RNA editing and contributes to nearly 90% of all editing events in human, we focused on this type of editing.
2. Understanding ADeditome's annotation categories
Search page, example: SERPINA3
- Input query: Official HUGO gene symbol or Entrez gene ID.
Gene search result page
Select your gene from the gene list.
Gene annotation result page
These are ADeditome's annotation categories for your query with links to their corresponding annotation parts.
1) Gene summary category
This category shows the information of the RNA edited gene. Firstly, it shows each partner gene's overall information from basic information such as symbol, alias, and locations and ENST accessions. This table also shows the tissue and cancer type information including manually curated PubMed article information.
2) 'RNA A-to-I editing events' category
This category provides the detailed RNA editing event information including genomic location from the UCSC genome browser, distribution of editing frequency across 9 brain tissues, and differential RNA editing events in AD not in control.
3) 'RNA A-to-I editing positional annotations' category
This category provides the annotation by coding/repeatitive regions and gene structure related annotations.
4) 'RNA A-to-I editing events in the alternative splicing sites' category
This category provides the RNA editing information located in the alternative splicing sites and the differential PSI values between RNA edited and non-edited samples.
5) 'Differntial gene expression between RNA A-to-I edited versus non-edited samples' category
This category provides the RNA editing information located in the alternative splicing sites and the differential PSI values between RNA edited and non-edited samples.
6) 'Protein coding region RNA A-to-I editings' category
This category provides the editing positioning information across the main protein domains with lollipop plots.
7) 'The effects of the RNA editing to the miRNA binding sites' category
This category provides the potential effects of RNA editing relating to microRNA specificity. If the RNA editing happened in miRNA, lncRNA, or mRNA, the binding of miRNA will be different.
8) 'The effects of the RNA editing to the stability of the RNA structures' category
This category provides the potential effects of RNA editing to the RNA secondary structures.
9) 'Relation with ADAR' category
This category provides the correlation between ADAR gene expression and RNA editing frequency/gene expressions.
10) 'Relation with AD stages' category
This category provides the correlation between AD stages and RNA editing frequency/gene expressions.
11) 'Related drugs and diseases with this gene' category
This table provides the DrugBank information of approved drugs related with RNA edited gene. Next table provides disease information related to the RNA edited gene.
3. Download data and contact us
Please go to download page and contact page.
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