We are very excited to join forces with MLCommons and OctoML.ai! Contact Grigori Fursin for more details!

Analysis of Triplet Motifs in Biological Signed Oriented Graphs Suggests a Relationship Between Fine Topology and Function

lib:ff2ed218d432ebcf (v1.0.0)

Authors: Alberto Calderone,Gianni Cesareni
ArXiv: 1803.06520
Document:  PDF  DOI 
Abstract URL: https://arxiv.org/abs/1803.06520v4


Background: Networks in different domains are characterized by similar global characteristics while differing in local structures. To further extend this concept, we investigated network regularities on a fine scale in order to examine the functional impact of recurring motifs in signed oriented biological networks. In this work we generalize to signaling net works some considerations made on feedback and feed forward loops and extend them by adding a close scrutiny of Linear Triplets, which have not yet been investigate in detail. Results: We studied the role of triplets, either open or closed (Loops or linear events) by enumerating them in different biological signaling networks and by comparing their significance profiles. We compared different data sources and investigated the fine topology of protein networks representing causal relationships based on transcriptional control, phosphorylation, ubiquitination and binding. Not only were we able to generalize findings that have already been reported but we also highlighted a connection between relative motif abundance and node function. Furthermore, by analyzing for the first time Linear Triplets, we highlighted the relative importance of nodes sitting in specific positions in closed signaling triplets. Finally, we tried to apply machine learning to show that a combination of motifs features can be used to derive node function. Availability: The triplets counter used for this work is available as a Cytoscape App and as a standalone command line Java application. http://apps.cytoscape.org/apps/counttriplets Keywords: Graph theory, graph analysis, graph topology, machine learning, cytoscape

Relevant initiatives  

Related knowledge about this paper Reproduced results (crowd-benchmarking and competitions) Artifact and reproducibility checklists Common formats for research projects and shared artifacts Reproducibility initiatives

Comments  

Please log in to add your comments!
If you notice any inapropriate content that should not be here, please report us as soon as possible and we will try to remove it within 48 hours!