Protein function prediction from dynamic protein interaction network using gene expression data

Computational prediction of functional annotation of proteins is an uphill task. There is an ever increasing gap between functional characterization of protein sequences and deluge of protein sequences generated by large-scale sequencing projects. The dynamic nature of protein interactions is frequently observed which is mostly influenced by any new change of state or change in stimuli. Functional characterization of proteins can be inferred from their interactions with each other, which is dynamic in nature. In this work, we have used a dynamic protein–protein interaction network (PPIN), time course gene expression data and protein sequence information for prediction of functional annotation of proteins. During progression of a particular function, it has also been observed that not all the proteins are active at all time points. For unannotated active proteins, our proposed methodology explores the dynamic PPIN consisting of level-1 and level-2 neighboring proteins at different time points, filtered by Damerau–Levenshtein edit distance to estimate the similarity between two protein sequences and coefficient variation methods to assess the strength of an edge in a network. Finally, from the filtered dynamic PPIN, at each time point, functional annotations of the level-2 proteins are assigned to the unknown and unannotated active proteins through the level-1 neighbor, following a bottom-up strategy. Our proposed methodology achieves an average precision, recall and F-Score of 0.59, 0.76 and 0.61 respectively, which is significantly higher than the reported state-of-the-art methods.