Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

6.7 Isoform Differential Expression Results
· METTL13: two reads mapping on alternative 3'UTRs;
· TSC22D2: two reads mapping on alternative 3'UTRs;
· RSRC2: two reads mapping on alternative 3'UTRs;
· TPM1: one read maps on the longest 3'UTR and the other on an internal
exon that is alternatively spliced in one isoform.
We used the GenemiR package described in chapter 8 to find out how many
genes, out of the 2,682 and 2,040 genes with differentially expressed isoforms,
were predicted to harbour the same microRNA targeting sites in their 3'UTRs.
The functionalities at the core of the GenemiR software package are to output
a list of microRNAs when a list of genes is inputted and, vice versa, to output
a list of genes when a list of microRNAs is inputted. The database used by
these core functionalities consists of all the microRNA to mRNA predictions
made by a maximum of eight leading algorithms and it varies in size depend-
ing on which algorithms the user has chosen to select as part of a specific
search. The search performed in this instance made use of the union of the
microRNA predictions from five of the most widely accepted target prediction
algorithms: PicTar [247], PITA [224], Targetscan [272], miRanda [213] and
DIANA-microT [315,316]. The choice of using the union set of the results
from the five prediction algorithms as opposed to the intersection set is justi-
fied by the fact that the intersection set for each of the two lists of over 2,000
genes is null. In fact, as explained in chapter 8, the algorithms available to
predict microRNA to mRNA interactions generate such different outputs that
it is extremely rare to have all of them agree on the predictions (granted, of
course, that the list of genes is not so large that finding an intersection set
becomes statistically possible, or that the number of prediction algorithms se-
lected are less than 3). When inputted into GenemiR, the 2,682 genes we found
with the parametric method, yielded a list of 5,016 microRNAs. Similarly, the
2,040 genes we found with the logarithmic (non-parametric) method, yielded
a list of 4,463 microRNAs. When the two lists of microRNAs were intersected
(2,358 microRNAs) and inputed again into the GenemiR package to find the
genes targeted by those microRNAs, we found 765 genes to be regulated by
the intersected list of microRNAs (Fig 6.17). Table 6.7 shows the microRNA
predictions resulting from the GenemiR query, stratified by prediction algo-
rithm and origin of the gene list - parametric vs. non-parametric method - as
well as the results that are common to both methods and unique to each.
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