EGIA- Evolutionary optimisation of Gene regulatory networks, an Integrative Approach

Abstract Quantitative modelling of gene regulatory networks (GRNs) is still lim-ited by data issues such as noise and the restricted length of available time series, creating an under-determination problem. However, large amounts of other types of biological data and knowledge are available, such as knockout experiments, anno-tations and so on, and it has been postulated that integration of these can improve model quality. However, integration has not been fully explored to date. Here, we present a novel integrative framework for different types of data that aims to en-hance model inference. This is based on evolutionary computation and uses differ-ent types of knowledge to introduce a novel customised initialisation and mutation operator and complex evaluation criteria, used to distinguish between candidate models. Specifically, the algorithm uses information from (i) knockout experiments, (ii) annotations of transcription factors, (iii) binding site motifs (expressed as posi-tion weight matrices) and (iv) DNA sequence of gene promoters, to drive the al-gorithm towards more plausible network structures. Further, the evaluation basis is also extended to include structure information included in these additional data. This framework is applied to both synthetic and real gene expression data. Models obtained by data integration display both quantitative and qualitative improvement