MOA2010-05_4_degradomics_Degradome-Seq_targets-sRNA

Version 1

Experimentally validated targets of endogenous sRNAs by Degradome-Seq. For each identified interaction, miRNAs/phasiRNA ID, the target transcript identifiers, representative gene identifier, full descriptions, and MapMan ontology annotations (GoMapMan; (Ramšak et al., 2014)) are shown. Short names for potato genes were inferred from Arabidopsis thaliana orthologs where applicable, else the StNIB_v1 gene identifier was set (Ramšak et al., 2014). For each sRNA-target interaction, degradome category are given: Category ‘0’ is defined as > 1 raw read at the position, with abundance at a position equal to the maximum on the transcript, and with only one maximum on the transcript. Category ‘1’ is described as > 1 raw read at the position, with abundance at the position equal to the maximum on the transcript, and more than one maximum position on the transcript. Category ‘2’ includes > 1 raw read at the position, and abundance at the position less than the maximum but higher than the median for the transcript. Category ‘3’ comprised the transcripts with > 1 raw read at the position, and abundance at the position equal to or less than the median for the transcript (Addo-Quaye et al., 2009). For each sRNA-target interaction also p-value (the chance is the total number of peaks of the given category divided by the effective transcriptome size, where 'n' is the number of transcripts), T_Start (one-based start position of the alignment within the transcript, T_Stop (one-based stop position of the alignment within the transcript), T_SLice (one-based position of the alignment opposite position 10 of the query, MFE_perfect (Minimum free energy of a perfectly matched site), MFE_site (Minimum free energy of the alignment), MFE_ratio (MFE_site / MFE_perfect) and number of mismatches are given. Additionally, for each sRNA the log2FC and p-values among different comparisons are given and the log2FC ratios of target transcripts between PVYNTN and mock inoculated Désirée or NahG-Désirée plants; yellow – upregulated, blue – downregulated, – statistically not significant (FDR p > 0.05). NA – not analyzed or not available. D – Désirée; NahG – NahG-Désirée; M – mock; P – PVYNTN.