Neighbourhoods in the yeast regulatory network in different physiological states

Motivation: The gene expression regulatory network in yeast controls the selective implementation of the information contained in the genome sequence. We seek to understand how, in different physiological states, the network reconfigures itself to produce a different proteome. Results: This article analyses this reconfiguration, focussing on changes in the local structure of the network. In particular, we define, extract and compare the 1-neighbourhoods of each transcription factor, where a 1-neighbourhood of a node in a network is the minimal subgraph of the network containing all nodes connected to the central node by an edge. We report the similarities and differences in the topologies and connectivities of these neighbourhoods in five physiological states for which data are available: Cell cycle, DNA damage, stress response, diauxic shift and sporulation. Based on our analysis, it seems apt to regard the components of the regulatory network as 'software', and the responses to changes in state, 'reprogramming'.

This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record, Arthur M Lesk, Arun S Konagurthu, “Neighbourhoods in the yeast regulatory network in different physiological states,” Bioinformatics, Volume 37, Issue 4, 15 February 2021, Pages 551–558, is available online at:


  • submitted.pdf

    size: 178 KB | mime_type: application/pdf | date: 2021-11-16


Work Title Neighbourhoods in the yeast regulatory network in different physiological states
Open Access
  1. Arthur M. Lesk
  2. Arun S. Konagurthu
License In Copyright (Rights Reserved)
Work Type Article
  1. Bioinformatics
Publication Date December 11, 2020
Publisher Identifier (DOI)
Deposited November 16, 2021




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Version 1

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  • Added submitted.pdf
  • Added Creator Arthur M. Lesk
  • Added Creator Arun S. Konagurthu
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