Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks

Abstract

Cellular processes are typically carried out by protein complexes and functional modules. Identifying them plays an important role for our attempt to reveal principles of cellular organizations and functions. In this article, we review computational algorithms for identifying protein complexes and/or functional modules from protein-protein interaction (PPI) networks. We first describe issues and pitfalls when interpreting PPI networks. Then based on types of data used and main ideas involved, we briefly describe protein complex and/or functional module identification algorithms in four categories: (i) those based on topological structures of unweighted PPI networks; (ii) those based on characters of weighted PPI networks; (iii) those based on multiple data integrations; and (iv) those based on dynamic PPI networks. The PPI networks are modelled increasingly precise when integrating more types of data, and the study of protein complexes would benefit by shifting from static to dynamic PPI networks.

Predicting Protein Complexes in Weighted Dynamic PPI Networks Based on ICSC

“…. , ; (9) while iter ≤ maxiter do (10) for = 1 to (11) Generation cuckoos : each V ∈ , if V ∉ Nest(:, :, ) then insert V into Cuckoo end if (12) for each cuckoo ∈ Cuckoo do (13) for each nest ∈ Nest(:, :, ) do (14) Calculate closeness(cuckoo , nest ); (15) if closeness(cuckoo , nest ) > 0 then (16) Roulette wheel selection , set nest = union(nest , cuckoo ); (17) Calculate objective function (nest ); (18) if (nest ) > (nest ) then (19) insert cuckoo into nest ; (20) end if (21) end if (22) end for (23) end for (24) Calculate the objective function (Nest(:, :, )) (25) end for (26) Find the largest objective function max = max( (Nest(:, :, ))), = 1, 2, . .…”

“…The biological processes are dynamic and PPIs are changing over time [14]. Therefore, it is necessary to shift the study of protein complexes from static PPI networks to the dynamic characteristics of PPI networks [15]. Wang et al constructed dynamic PPI network based on time series gene expression data to detect protein complexes [16].…”

Combining sequence and Gene Ontology for protein module detection in the Weighted Network

“…In (Chen et al, 2014;Wu et al, 2009), a detected cluster is assumed to match a known complex if its overlapping score is at least 0.2, which is also adopted in this study. For comparison, recall, precision and f-measure are adopted, recall and precision Lin, 1998;project;Wu et al, 2009) are defined in (10) and (11):…”

“…F-measure (Chen et al, 2014;Li et al, 2010), as the harmonic mean of precision and recall, can be used to evaluate the overall performance in (12):…”

“…A biological network manifests a modular organization and consists of different functional modules. Much of a cell's activity is organized as a network composed of lots of the interacting modules (Chen et al, 2014;Segal et al, 2003), and altering the connections between the different modules may affect changes in cellular properties and functions. A protein module, composed of interdependencies of proteins, is a group of proteins giving rise to the target-specific function whose function is separable from those of other modules (Sharma et al, 2015).…”