Overview

Regulatory Snapshots is a method to identify regulatory modules composed of genes exhibiting coherent transcriptional activity in a specific time interval and their transcription factors.

Regulatory Snapshots is described in the following article:
Gonçalves JP, Aires RS, Francisco AP, and Madeira SC. Regulatory Snapshots: Integrative Mining of Regulatory Modules from Expression Time Series and Regulatory Networks, PLoS ONE 2012, 7(5):e35977.
[full text html] [full text pdf] [cite it] doi:10.1371/journal.pone.0035977

 
Method

Regulatory modules are discovered in two steps:

  1. Identification of temporal transcriptional modules: time-aware biclustering step to uncover subsets of genes with coherent behavior spanning a subset of consecutive time points;
  2. Prioritization of transcription factors targeting the modules at each time point: personalized ranking on the transpose of the regulatory network graph taking as input signal the expression level of the genes in each transcriptional module at each time point.

Visual representations, called regulatory snapshots after the method's name, are also depicted for each regulatory module, containing the transcriptionally coherent genes and their most relevant transcription factors at each time point. Regulatory Snapshots expose the evolution of the regulatory activity in the module over time.

 
Case study

In one of the case studies, we used Regulatory Snapshots to unravel and characterize regulatory modules underlying Saccharomyces cerevisiae's response to heat shock. Results can be easily reproduced using our software tools BiGGEsTS and Regulatory Snapshots as described in the tutorial section.