This article is part of the supplement: Ninth International Conference on Bioinformatics (InCoB2010): Computational Biology
Proceedings
RNA editing of nuclear transcripts in Arabidopsis thaliana
1 Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
2 State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
3 Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
BMC Genomics 2010, 11(Suppl 4):S12 doi:10.1186/1471-2164-11-S4-S12
Published: 2 December 2010Additional files
Additional file 1 - Data S1 Edited sites in protein-coding genes in Arabidopsis (only the editing sites resided in mRNAs were considered):
Prediction criteria: more than two candidate editing sites should be present in one transcript and each editing site must be supported by more than five distinct short-read sequences.
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Additional file 2 - Data S2 Editing sites in pre-miRNAs in Arabidopsis:
Prediction criteria: each editing site in one pre-miRNA should be supported by more than two distinct short-read sequences.
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Additional file 9:
Data S7 Detailed information of the MPSS and PARE data utilized in this study.
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Additional file 3:
Data S3 100-nt sequences surrounding the editing sites in protein-coding genes, which were utilized for conserved element detection. The random sequences for control analysis are included.
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Additional file 4:
Data S4 Results of searching for conserved elements surrounding the editing sites in protein-coding genes. The results of three replicates of control analysis are included.
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Additional file 5:
Data S5 Result of GO term enrichment analysis of edited protein-coding genes in Arabidopsis.
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Additional file 6:
Figure S1 Clustering analysis of RNA editing sites.
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Additional file 7:
Data S6 Codon variation by RNA editing in nuclear protein-coding genes (only the edited codons resided in CDSs were considered).
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Additional file 8:
Figure S2 Secondary structure transformation of edited ath-MIR854a, ath-MIR854b, and ath-MIR854d.
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