Comparison of prediction accuracy under the precision metric.

<p>The fraction of training sets <i>f</i> is varied from 0.5 to 0.9.</p

Demonstration of using rows of A + I as the feature vectors for nodes.

<p>In the network, nodes 4 and 5 are topologically equivalent. However, the 4th row of <b>A</b> reads [0, 1, 1, 0, 1], and the 5th reads [0, 1, 1, 1, 0], which are different. By adding <b>I</b>, the 4th and 5th rows of <b>A</b> + <b>I</b> now are both [0, 1, 1, 1, 1], which is exactly what we want. This is also the case for nodes 2 and 3. The <i>k</i>-th feature of a node can be interpreted as whether the distance between it and node <i>k</i> is no more than 1. For example, the distance between node 1 and 4 is greater than 1, while the distance between all the other nodes and node 4 are within 1, so the 4th feature is [0, 1, 1, 1, 1]^<i>T</i>.</p

Prediction accuracy with different cutoff threshold <i>t</i> in the proposed noise-filtering method.

<p>The symbol <i>f</i> denotes the fraction of links in the training sets.</p

Additional file 9: Table S9. of Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing

KEGG pathways of significantly down-regulated genes in the drought-tolerant tomato IL9–1. (XLSX 14 kb

Additional file 8: Table S8. of Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing

KEGG pathways of significantly down-regulated genes in the drought-sensitive tomato M82. (XLSX 18 kb

Additional file 17: Table S17. of Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing

Expression level of the target genes for the differentially-expressed novel miRNAs identified. (XLSX 45 kb

Additional file 13: Table S13. of Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing

Expression level of the target genes for the differentially-expressed conserved miRNAs identified. (XLSX 29 kb

Venn diagrams showing number and overlap of differentially expressed genes under cold stress in LA1777, LA3969, and LA4024.

<p>(A) Number of up-regulated genes (log₂ ratio stress/control≥2 and q-value<0.05). (B) Number of down-regulated genes (log₂ ratio stress/control≤−2 and q-value<0.05). The number in parentheses indicates the total number of genes up- or down-regulated by cold stress in each genotype.</p

Significantly altered biochemical pathways and their corresponding gene expression between tolerant and sensitive tomato genotypes under cold stress.

<p>The 92 genes with significant differences in expression between tolerant and sensitive genotypes at 3 d of cold treatment (4°C) were analyzed for significantly (p<0.05) altered biochemical pathways using the Plant MetGenMAP system <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050785#pone.0050785-Joung1" target="_blank">[33]</a>. (A) Positive (up-regulated) and negative (down-regulated) expression values (log₂ ratio cold stress/control) are means of three independent biological replicates.</p

Chromosomal distribution of genes differentially expressed between the tolerant and sensitive genotypes under cold stress.

<p>Each horizontal line represents one gene. The red lines represent the 92 genes (as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050785#pone.0050785.s001" target="_blank">Figures S1</a>) with significant difference in expression between the two tolerant and sensitive genotypes under cold stress. The blue lines represent the 126 genes (as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050785#pone.0050785.s006" target="_blank">Table S2</a>) whose expression level in LA1777 is significantly different from that in LA3969 and LA4024. The yellow regions on chromosomes indicated the introgressed chromosomal regions of the 22 selected cold-tolerant ILs and/or cold tolerance QTLs identified previously in <i>S. habrochaites </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050785#pone.0050785-Goodstal1" target="_blank">[7]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050785#pone.0050785-Vallejos1" target="_blank">[12]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050785#pone.0050785-Truco1" target="_blank">[13]</a>. Chromosome numbers are indicated at the top of each bar. Question mark indicates probe sequence dose not match on chromosome.</p