Dataset Information

Motifs enable communication efficiency and fault-tolerance in transcriptional networks.

ABSTRACT: Analysis of the topology of transcriptional regulatory networks (TRNs) is an effective way to study the regulatory interactions between the transcription factors (TFs) and the target genes. TRNs are characterized by the abundance of motifs such as feed forward loops (FFLs), which contribute to their structural and functional properties. In this paper, we focus on the role of motifs (specifically, FFLs) in signal propagation in TRNs and the organization of the TRN topology with FFLs as building blocks. To this end, we classify nodes participating in FFLs (termed motif central nodes) into three distinct roles (namely, roles A, B and C), and contrast them with TRN nodes having high connectivity on the basis of their potential for information dissemination, using metrics such as network efficiency, path enumeration, epidemic models and standard graph centrality measures. We also present the notion of a three tier architecture and how it can help study the structural properties of TRN based on connectivity and clustering tendency of motif central nodes. Finally, we motivate the potential implication of the structural properties of motif centrality in design of efficient protocols of information routing in communication networks as well as their functional properties in global regulation and stress response to study specific disease conditions and identification of drug targets.

SUBMITTER: Roy S

PROVIDER: S-EPMC7296022 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Motifs enable communication efficiency and fault-tolerance in transcriptional networks.

Roy Satyaki S Ghosh Preetam P Barua Dipak D Das Sajal K SK

Scientific reports 20200615 1

Analysis of the topology of transcriptional regulatory networks (TRNs) is an effective way to study the regulatory interactions between the transcription factors (TFs) and the target genes. TRNs are characterized by the abundance of motifs such as feed forward loops (FFLs), which contribute to their structural and functional properties. In this paper, we focus on the role of motifs (specifically, FFLs) in signal propagation in TRNs and the organization of the TRN topology with FFLs as building b ...[more]

PMID: 32541819

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Project description:Considering the Internet of Things (IoT) impact in today's world, uninterrupted service is essential, and recovery has received more attention than ever before. Fault-tolerance (FT) is an essential aspect of network resilience. Fault-tolerance mechanisms are required to ensure high availability and high reliability in systems. The advent of software-defined networking (SDN) in the IoT plays a significant role in providing a reliable communication platform. This paper proposes a data plane fault-tolerant architecture using the concepts of software-defined networks for IoT environments. In this work, a mathematical model called Shared Risk Link Group (SRLG) calculates redundant paths as the primary and backup non-overlapping paths between network equipment. In addition to the fault tolerance, service quality was considered in the proposed schemes. Putting the percentage of link bandwidth usage and the rate of link delay in calculating link costs makes it possible to calculate two completely non-overlapping paths with the best condition. We compare our two proposed dynamic schemes with the hybrid disjoint paths (Hybrid_DP) method and our previous work. IoT developments, wireless and wired equipment are now used in many industrial and commercial applications, so the proposed hybrid dynamic method supports both wired and wireless devices; furthermore multiple link failures will be supported in the two proposed dynamic schemes. Simulation results indicate that, while reducing the error recovery time, the two proposed dynamic designs lead to improved service quality parameters such as packet loss and delay compared to the Hybrid_DP method. The results show that in case of a link failure in the network, the proposed hybrid dynamic scheme's recovery time is approximately 12 ms. Furthermore, in the proposed hybrid dynamic scheme, on average, the recovery time, the packet loss, and the delay improved by 22.39%, 8.2%, 5.66%, compared to the Hybrid_DP method, respectively.

Dataset Information

Motifs enable communication efficiency and fault-tolerance in transcriptional networks.

Publications

Motifs enable communication efficiency and fault-tolerance in transcriptional networks.

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