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Welcome to ExpEdit

RNA editing is a widespread post-transcriptional molecular phenomenon that can increase proteomic diversity, by modifying the sequence of completely or partially non-functional primary transcripts, through a variety of mechanistically and evolutionarily unrelated pathways [1]. Editing by base substitution has been investigated in animals, plants and viruses [2]. In human, the A-to-I substitution is the most frequent editing event, carried out by members of ADAR (adenosine deaminases acting on RNA) family [3]. Such alterations can be predicted by computational analyses based on the alignment of mRNA/EST sequences onto the genome of origin [4]. Recent high-throughput sequence technologies offer the unique opportunity to study entire transcriptomes in a variety of experimental conditions. Massive RNA sequencing, therefore, may facilitate the investigation of post-transcriptional mechanisms occurring herein.

In order to detect A-to-I editing sites in human supported by transcript data obtained by RNA-Seq experiments we developed the web application ExpEdit. In our system, mapping data (in SAM/BAM format) or directly sequence reads (in FASTQ or SRA format) can be provided as input to carry out a comparative analysis against a large collection of known editing sites collected in DARNED database [5] as well as other user-provided potentially edited positions.

References:

1. Gott, J.M. and Emeson, R.B. (2000) Annual review of genetics, 34, 499-531 PMID: 11092837

2. Casey, J.L. (2006) Current topics in microbiology and immunology, 307, 67-89 PMID: 16903221

3. Keegan, L.P., Gallo, A., O'Connell, MA. (2001) The many roles of an RNA editor. Nature Review Genetics, 2(11):869-78 PMID: 11715042

4. Levanon, E.Y. et al. (2004) Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nature Biotechnology, 22(8):1001-5 PMID:15258596

5. Kiran A. and Baranov, PV. (2010) DARNED: a DAtabase of RNa EDiting in humans. Bioinformatics, 15;26(14):1772-6 PMID: 20547637

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