Link Clustering Reveals Structural Characteristics and Biological Contexts in Signed Molecular Networks

Abstract

Many biological networks are signed molecular networks which consist of positive and negative links. To reveal the distinct features between links with different signs, we proposed signed link-clustering coefficients that assess the similarity of inter-action profiles between linked molecules. We found that positive links tended to cluster together, while negative links usually behaved like bridges between positive clusters. Positive links with higher adhesiveness tended to share protein domains, be associated with protein-protein interactions and make intra-connections within protein complexes. Negative links that were more bridge-like tended to make interconnections between protein complexes. Utilizing the proposed measures to group positive links, we observed hierarchical modules that could be well characterized by functional annotations or known protein complexes. Our results imply that the proposed sign-specific measures can help reveal the network structural characteristics and the embedded biological contexts of signed links, as well as the functional organization of signed molecular networks.

Modulus consensus in discrete-time signed networks and properties of special recurrent inequalities

“…The protocol (10) has been proposed in the influential paper [44] (see also [46]), dealing with distributed optimization problems. The special cases of protocols (11) and (12) naturally arise in distributed algorithms, solving linear equations, see respectively [47], [48] and [49]; a randomized version of (12) has been also examined in [45]. Theorem 5: Let the set Ξ i be closed and convex, and assume that Ξ = Ξ 1 ∩ .…”

“…One reason for clustering in multi-agent networks is the presence of "negative" (repulsive, antagonistic) interactions among the agents [8]. Models of signed (or "coopetition") A networks with positive and negative couplings among the nodes describe a broad class of real-world systems, from molecular ensembles [12] to continental supply chains [13]. Positive and negative relations among social actors can express, respectively, trust (friendship) or distrust (hostility).…”

Functional Analysis and Characterization of Differential Coexpression Networks

“…Coexpression network can be considered as a signed network that consists of positive (correlation) and negative (anti-correlation) links. Since correlations have transitive characteristics, two genes with common coexpressed and/or anti-coexpressed gene are expected to express simultaneously 25 . In terms of triad, which consists of three mutually linked nodes and is the smallest unit of a complete graph, a signed network generally contains four types of triads 25 .…”

“…Since correlations have transitive characteristics, two genes with common coexpressed and/or anti-coexpressed gene are expected to express simultaneously 25 . In terms of triad, which consists of three mutually linked nodes and is the smallest unit of a complete graph, a signed network generally contains four types of triads 25 . However, the transitive property of coexpression links indicates that only two types of triads can be observed in the coexpression network, that is, triads with an odd number of positive links 25 .…”

Estudo dinâmico da expressão gênica global durante a interação STEC-enterócito utilizando séries temporais

“…Em E. coli SlyA induz a expressão do gene hlyE, que codifica para a toxina hemolisina E (Spory et al, 2002). Oltvai, 2004;Liu et al, 2012;Lin et al, 2013). Estes resultados sugerem que EH41 é capaz de induzir uma intensa desregulação genômica no enterócito.…”