Targets of PVY-derived siRNAs identified by Degradome-Seq. For each predicted interaction, PVYNTN-derived siRNAs (vsiRNAs), 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 vsiRNA-target interaction, degradome category (Addo-Quaye et al., 2009), its 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, 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.
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Created: 4th Mar 2019 at 17:20
Last updated: 4th Mar 2019 at 17:32
Last used: 24th Jun 2019 at 17:50