Finally, the underlying datasets as well as all predictions in the study are available for download from an online web-server.
As reported in Figure 6, we found a small (but significant) depletion of predictions near the 3' end of protein-coding genes as well as depletion of predictions in the first intron.
For each prediction, the same information as for predictions in the reference 3′-UTRs was recorded.
The top-scoring rejected junctions are saved for reporting as marginal predictions in the output.
Next, EVC and EVC2 orthologues were each found as gene predictions in the genome assemblies of amphioxus (Branchiostoma floridae), sea urchin (Strongylocentrotus purpuratus), gastropod snail (Lottia gigantea) and sea anemone (Nematostella vectensis).
This strategy is used in both the MCL implementation of gene family prediction mclblast as well as in the prediction of clusters of orthologous genes in orthoMCL [ 29].
This indicates that the predictions during meal absorption are less reliable as compared with predictions in the fasted state.
We refer to significant chemical-gene set associations to gene expression data as "associations" or "predictions" in the following.
Simulation results are compared in steady-state as well as transient predictions in order to determine the required complexity of the model to yield accurate results.
The predicted affinity was then determined as the average of the 15 predictions in the neural network ensembles.
