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The IPA Upstream Regulator and Downstream Effects Analysis enabled the prediction of regulators that may be driving the altered protein expression patterns seen.
This illustrates a coordinated prediction of regulators of chemotactic and inflammatory response such as IL6 and CXCL10, interferon and antiviral response (Additional File 8).
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Systems based modular approaches were also extensively used for gene annotation, protein function prediction, identification of regulators and novel proteins in molecular pathways in yeast [ 22]–[ 27].
We were able to perform a reverse prediction of the regulators for the selected clusters of co-regulated genes and to suggest a number of expected functional links/potential regulators of the cluster of co-expressed genes relevant to translation.
We have used the 3 pre-selected gene groups with known regulators (Table 2) to test our algorithm on prediction of potential regulators.
We show that taking into account genetic distance data is requisite in the prediction of candidate regulators of trans-eQTL clusters.
It is also informative in the prediction of key regulators.
Integrating binding sites with transcription factor conservation patterns also facilitated prediction of putative regulators for one of the binding sites.
Prediction of upstream regulators that could potentially control several of the differentially expressed proteins yielded four molecules with high activation scores (Table 2).
However the genetic interaction network can be used much more efficiently with the SPF method in prediction of potential regulators of gene expression.
The directionality information provided by those methods can be incorporated into network interrogation to generate more accurate prediction of key regulators.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com