Figure 2

Main sections provided in the NexGenEx- platform query form. 1) Genome: the genome of interest, e.g. Tomato, 2) Reference: it indicates the reference genotype or cultivar sequences of interest, e.g. Solanum lycopersicum cv Heinz, version 2.40; 3) NGS collections available in the platform, e.g. the Heinz Illumina based RNA-seq collection in physiological condition; 4) link to the data source and paper for this collection; 5) available libraries (replicates/stages/tissues) included in the collection; 6) Feature type: represents the reference genome feature selected for read counting (e.g. mRNA, represents the exons in the locus); 7) Normalization method; 8) Matrix peak coloring, which defines the approach for color coding of the expression levels. This option assigns color frequencies to the cells of a heatmap view comparatively with the expression levels within the query result set (local ) or within the whole selected libraries (global ). 9) Transformation method: expression levels or their log2 transformed results can be accessed; 10) Correlation method: Pearson product–moment correlation coefficient or Spareman’s correlation coefficient or Both; 11) Replicate view: defines the expression level by each libraries (Separate) or averaged between identical replicates (Average); 12) Heatmap coloring: different heatmap coloring combinations are provided for expression level visualization; 13) Search in: searchable fields can be one/multiple locus ids (IDs), or simple/multiple functional keywords with advanced selection options (Keyword), or genome regions (Region), and 14) the search area (Locus IDs/Functional keyword/Region): is the text area in which IDs or functional keywords may be listed, or a specific region of the genome may be specified. Accepted formats are described in the information pop-up from the website interface. “Info” buttons are available to support the users.