NAUTICA: classifying transcription factor interactions by positional and protein-protein interaction information.

Publisher: BioMed Central Country of Publication: England NLM ID: 101258412 Publication Model: Electronic Cited Medium: Internet ISSN: 1745-6150 (Electronic) Linking ISSN: 17456150 NLM ISO Abbreviation: Biol Direct Subsets: MEDLINE

Original Publication: [London] : BioMed Central, 2006-

Protein Interaction Maps*; Molecular Biology/*instrumentation ; Transcription Factors/*chemistry; Binding Sites

Background: Inferring the mechanisms that drive transcriptional regulation is of great interest to biologists. Generally, methods that predict physical interactions between transcription factors (TFs) based on positional information of their binding sites (e.g. chromatin immunoprecipitation followed by sequencing (ChIP-Seq) experiments) cannot distinguish between different kinds of interaction at the same binding spots, such as co-operation and competition.
Results: In this work, we present the Network-Augmented Transcriptional Interaction and Coregulation Analyser (NAUTICA), which employs information from protein-protein interaction (PPI) networks to assign TF-TF interaction candidates to one of three classes: competition, co-operation and non-interactions. NAUTICA filters available PPI network edges and fits a prediction model based on the number of shared partners in the PPI network between two candidate interactors.
Conclusions: NAUTICA improves on existing positional information-based TF-TF interaction prediction results, demonstrating how PPI information can improve the quality of TF interaction prediction. NAUTICA predictions - both co-operations and competitions - are supported by literature investigation, providing evidence on its capability of providing novel interactions of both kinds.
Reviewers: This article was reviewed by Zoltán Hegedüs and Endre Barta.

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693174 International ERC_ European Research Council; T1 251RES1725 International Ministry of Education - Singapore

Keywords: Data-driven analysis; Interaction classification; Protein−protein interactions; TF-TF competition; Transcription factors

0 (Transcription Factors)

Date Created: 20200917 Date Completed: 20210811 Latest Revision: 20210811

20221213

PMC7493360

10.1186/s13062-020-00268-1

32938476