The pipeline of the whole approach.

<p>Our approach is mainly divided into two steps: Online prediction and local classification. PsRNATarget, TAPIR, UEA_sRNA were chosen to predict original miRNA target candidates in the first step. 99 experimentally validated miRNA target interactions are employed to serve as SVM positives in the second step. Moreover, 1618 degradome sequencing supported miRNA target interactions are collected for validation experiment.</p

Information of three online predictors for plant miRNA targets.

a<p>Accepttion of user-supplied transcripts.</p>b<p>Limitation for miRNA/transcript input.</p>c<p>Approximate running time.</p

Additional file 2: Table S2. of Inferring plant microRNA functional similarity using a weighted protein-protein interaction network

The clusters of the A. thaliana miRNAs. (DOCX 18 kb

Contrast information between <i>Arabidopsis thaliana</i> and other plant species.

a<p>Total number of miRNA.</p>b<p>miRNA target interactions gained by predictors.</p>c<p>miRNA target interactions predicted to be positives by PCA-SVM model.</p

Three categories of SVM features.

<p>A total of 48 features belonging to 3 categories are extracted to classify high quality miRNA target interactions from false positive ones. All features mentioned are widely accepted to predict miRNA-target interactions and discriminate creditable targets from false positive ones.</p

ROC curves of SVM and PCA-SVM.

<p>The ROC curves of classifiers created on 48 original features (the blue solid line) and 25 features after PCA (the red dotted line).</p

The process of semi-supervised self-training.

<p>The whole approach can be generalized into an iteration process of training and predicting. Condition 1 tells if the sample confirms to the expansion rules. Condition 2 tells if all unlabeled data in test set are labeled by the classifier. Condition 3 tells if the candidate set contains samples with positive label and negative label at the same time.</p

Leave-one-out cross-validation on four kernels.

<p>The cross-validation approaches for different kernels were run on our training set including 198 samples. The accuracy was used to evaluate the performance.</p

Additional file 1: Table S1. of Inferring plant microRNA functional similarity using a weighted protein-protein interaction network

The families of the A. thaliana miRNAs. (DOCX 17 kb

Partial interactive network of miRNA and targets.

<p>This partial network consists of 4 miRNAs from ath-miR167 family and 18 miRNA-target interactions. Diamond and circular nodes represent miRNAs and target genes respectively. An edge represents a targeted relation.</p