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However, miRNAs removed from next miRBase releases were also excluded from the study.
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A list of targets of miRNAs for each dysregulated miRNA was generated from data extraction from Mirbase databse.
The seed sequences were extracted from miRNA sequences downloaded from miRBase 19 (http://microrna.sanger.ac.uk/).sanger.ac.uk/
Mature and mature-star miRNA sequences from plants were extracted from miRBase (release 16).
lncRNA coordinates are from [ 26], miRNA coordinates are from miRBase 19.
Each of our samples was assayed using an array (Genechip miRNA 2.0 Array) that is defined by 1,105 mature miRNAs, 1.105 pre-miRNAs, 32 scaRNA and 2,302 snoRNA from the miRBASE (v.15)).
The rice miRNA data including the precursor sequences and mature miRNAs were derived from the miRBase database (release 19.0).
The EBV miRNA sequences obtained from deep sequencing exhibited a high degree of deviation from their miRBase "reference" sequences.
Human miRNAs (hsa-miRNAs) were taken from the miRBase site (http://mirbase.org).org
Nucleotide sequences of human mature miR-1322 were downloaded from the miRBase database (http://mirbase.org) [ 13].
The miRNA sequences were from the miRBase version 5.
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