Distribution of conserved miRNA family members in potato.

<p>Graphical representation of the different members of conserved miRNA families found in potato by sequencing and bioinformatics prediction.</p

Summary of reads and unique sequences in small RNA libraries.

<p>Summary of reads and unique sequences in small RNA libraries.</p

Origin of miRNA precursors.

<p>The majority of miRNA precursors are transcribed from intergenic regions. miRNA precursors originating from coding regions locates mainly in introns.</p

Size distribution of small RNA sequences.

<p>(A) Reads and unique sequence distribution in all the small RNA libraries. 24 and 21nt length reads are the most abundant reads among the small RNAs. (B) Size distribution of reads originating from leaf (dark grey) and stolon (light grey) tissues expressed as a percentage of total reads. 24 and 21nt length reads are dominant in both of the tissues; in stolon tissues there are more reads for 21, 23 and 24nt length.</p

Flowchart for the prediction of miRNAs and their target RNAs in potato.

<p>Flowchart for the prediction of miRNAs and their target RNAs in potato.</p

Reads length analysis of the predicted unique miRNA and star (miRNA*) sequences.

<p>Graph shows that most miRNAs and star sequences have 24 and 21 nt length. Star sequences show different distribution compared to miRNAs; there are less star sequences with 17, 20, 21 and 24 nt length but more in other length categories.</p

Additional file 1: of Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size

File contains additional Figures and Tables. Figure S1. Bar plots of pAUROC values for top 1000 edge predictions. Figure S2. Bar plots of pAUROC values of top 1000 predictions for GNW3000 module-based. Figure S3. GNW settings for data simulation. Figure S4. Examples of evaluation results. Table S1. Summaries of evaluation of gene network inference methods. Table S2. R packages used to construct and evaluate GRNs. (DOCX 1867 kb

Additional file 2: of Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size

Configuration file for GeneNetWeaver (GNW). The settings in the file were load in GNW to generate synthetic data. (DOCX 28 kb

Differentially expressed genes on three superscaffolds under the tuber shape QTLs.

<p>Differentially expressed genes on three superscaffolds under the tuber shape QTLs.</p

Representation of GO term enrichment.

<p>Selected GO term enrichments are visualized in early (A) and late (B) leaf samples. Figs (C) and (D) show GO term enrichment for early and late tuber samples, respectively. Categories are indicated on Y axis, log10[1/p] is on the X-axis where p is the p-value of the enrichment.</p