An improved network alignment algorithm of dynamic protein interaction networks of floral development in Arabidopsis

To align the dynamic protein-protein interaction networks (DPINs) might help to better understand the molecular network genetic mechanisms of flower development in Arabidopsis thaliana. In this paper, the microarray data of flower development in Arabidopsis were obtained from the gene expression omnibus (GEO) database. The active expressed genes at each time point were screened using {sigma} method. The DPIN at each time point were reconstructed using search tool for the retrieval of interacting genes/proteins (STRING) and then visualized with Cytoscape, and enrichment analysis implemented using clusterProfiler package of the R language. We improved NetCoffee 2, a multi-time, multidimensional, and multi-level network alignment algorithm, NetCoffee 2+, was developed for floral development of A. thaliana. In this paper, a network alignment algorithm applied to A. thaliana, NetCoffee 2+, was developed, and the key proteins and protein complexes during floral development in A. thaliana were mined, with new potential ABCDE-like genes discovered.