Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

8.5 Target Prediction Ensemble Analysis Results
summarised in figure 8.4. We first run the method on the predictions from
each algorithm alone and then extended it to all combinations of prediction
algorithm results. The score E reflecting the accuracy of each prediction or
combination of predictions, ranges between 0 and 1 (0 > E > 1), with 1 re-
flecting a perfectly matching set of predictions between the algorithm being
evaluated and our experimental data. The score is calculated following these
successive steps:
1. filter out, for each prediction algorithm and for each microRNA exper-
imentally observed to be up-regulated, the genes that are predicted to
be target by that microRNA but are not present in the gene background
list;
2. generate a union list from the genes filtered in step 1 for the entire cohort
of up-regulated microRNAs, for each prediction algorithm;
3. iterate over each gene in the union list and increase a cumulative counter
every time the gene is predicted to be targeted by one of the up-regulated
microRNAs, for each prediction algorithm. This counter is normalised
to the number of microRNAs that the prediction contains from the list
of 258 experimentally measured microRNAs;
4. sort the union gene list by the count calculated in step 3 to generate a
"hit" list, representative of each prediction algorithm;
5. iterate over the hit list summing in a cumulative counter C1, the counts
associated to all the genes in the list, which have been predicted by the
prediction algorithm ;
6. iterate over the hit list summing in a cumulative counter C2, the counts
associated to the genes that are experimentally observed to be down-
regulated in our exon array data;
7. generate a score value by dividing the cumulative counters C1 and C2,
representing a measure of how well a prediction algorithm fared based
on how many genes it correctly predicted to be targeted in our GNS cell
lines, considering the same cell line expression profile as a background
for calculations.
Scores for each single prediction algorithm are listed in table 8.2 below. To
evaluate whether combinations of different algorithms were more accurate at
213