Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

8.4 Filters Results
8.3) is to allow the user to specify an appropriate range of return results from
each query, depending on either the numbers of different microRNAs expected
to play a role in gene regulation (adjusted according to the Minimum and
Cumulative filters), or the level of concordance the user enforces between the
combination of prediction algorithms defined. The user can at all times pref-
erentially select a desired subset of algorithms upon which prediction results
will be based and the two types of filters available - Minimum and Cumulative
- will be applied on the prediction results of those algorithms.
The consequence of setting the Minimum filter to a given value depends on
the type of query he user makes. If the query starts with a list of microRNAs
and therefore asks which genes are target by these microRNAs, according to a
number n of prediction algorithms, then setting the Minimum filter to a given
value returns a set of genes targeted by at least that number of microRNAs,
as reported by all of the selected algorithms. For example, if the inputted list
contains m = 10 microRNAs and n = 3 prediction algorithms are selected,
then the Minimum filter will range from one to 10 and setting it on four will
cause it to report only those genes that are targeted by at least eight microR-
NAs as predicted by each of the three algorithms alone. If the query were to
start from a list containing g = 30 genes and n = 3 prediction algorithms were
selected, then the Minimum filter would range from one to 30 and setting it
on 24 would cause it to report only those microRNAs that target 24 genes as
predicted by each of the prediction algorithms alone (Fig 8.3). The number of
genes returned from the query will therefore depend greatly on the prediction
algorithms selected.
The Cumulative filter acts in an alternative fashion: a gene is reported if
the total number of microRNA predictions, according to all of the chosen algo-
rithms, is at least equal to or greater than the minimum value set by the user.
This alleviates the requirement that every algorithm independently predict a
set number of microRNA interactions; rather, the aggregate sum of all results
in determining which target genes to report, will be considered. Using the
Cumulative filter is a less stringent approach and, all things equal, returns a
higher number of outputted results. For example, if the inputted list contains
m = 10 microRNAs and n = 3 prediction algorithms are selected, then the Cu-
mulative filter will range from one to 10x3 = 30 and setting it on 20 will cause
it to report the genes that are targeted by at least 20 microRNAs according
to any combination of prediction algorithms selected, without the requirement
that any particular algorithm predict a set threshold of microRNAs. If the
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