Combining expression-based features with sequence-based features boosts the predictive accuracy when only adopting sequence-based features for predicting all three domains of protein function.

<p>(a,d) the MCC and AUROC values obtained by different features for predicting biological process domain of GO terms over cross validation. (b,e) the MCC and AUROC values obtained by different features for predicting molecular function domain of GO terms over cross validation. (c,f) the MCC and AUROC values obtained by different features for predicting cellular component domain of GO terms over cross validation.</p

GO terms obtained most improvement on predictive performance by FFPred-fly+.

<p>GO terms obtained most improvement on predictive performance by FFPred-fly+.</p

Distribution of related feature importance value for features denoting each of main developmental stages for <i>Drosophila</i>.

<p>(a) the distribution of RFI values for predicting biological process domain of GO terms; (b) the distribution of RFI values for predicting moleulcar function domain of GO terms; (c) the distribution of RFI values for predicting cellular component domain of GO terms.</p

FFPred-fly+ shows higher predictive accuracy comparing with using InterPro database for predicting biological process and cellular component domains of protein function.

<p>(a) FFPred-fly+ obtains higher MCC values on predicting all 301 GO terms; (b) FFPred-fly+ obtains higher MCC values on predicting 196 biological process domain of GO terms; (c) Using InterPro database obtains better MCC values on predicting 68 molecular function domain of GO terms; (d) FFPred-fly+ obtains higher MCC values on predicting 37 cellular component domain of GO terms.</p

Expression profiles of three transcripts for gene FBgn0067864; the average expression profile over three transcripts (i.e. the red line); and the expression profile for the main-transcript (i.e. the black line).

<p>Expression profiles of three transcripts for gene FBgn0067864; the average expression profile over three transcripts (i.e. the red line); and the expression profile for the main-transcript (i.e. the black line).</p

Expression-based features show competitive performance against the sequence-based features for predicting the biological process domain of protein function.

<p>(a,d) the MCC and AUROC values obtained by different features for predicting the biological process domain of GO terms over cross validation. (b,e) the MCC and AUROC values obtained by different features for predicting the molecular function domain of GO terms over cross validation. (c,f) the MCC and AUROC values obtained by different features for predicting the cellular component domain of GO terms over cross validation.</p

FFPred-fly+ shows better performance than FFPred-fly when predicting all three domains of protein function.

<p>(a,b) FFPred-fly+ obtains higher MCC and AUROC values on predicting all 301 GO terms; (c,d) FFPred-fly+ obtains higher MCC and AUROC values on predicting 196 biological process GO terms; (e,f) FFPred-fly+ obtains similar MCC values but higher AUROC values on predicting 68 molecular function GO terms; (g,h) FFPred-fly+ obtains similar MCC values but higher AUROC values on predicting 37 cellular component GO terms.</p

The distribution of RFI values for predicting 10 specific development-associated GO terms.

<p>(a) The heatmap of relative feature importance on predicting development-related BP terms by Random Forests classification algorithm; (b) regulation of nervous system development (GO:0051960); (c) eye morphogenesis (GO:0048592); (d) cell morphogenesis (GO:0000902); (e) cell migration (GO:0016477).</p

Validated proteins predicted by FFPred-fly+.

<p>Validated proteins predicted by FFPred-fly+.</p

Mean AUROC values obtained by different expression-based feature groups and the sequence-based feature group over cross validation.

<p>Mean AUROC values obtained by different expression-based feature groups and the sequence-based feature group over cross validation.</p