Tools To Reconstruct The Transcription Regulatory Circuits

Question

[Biostar User]

What are commonly used tools to reconstruct the transcription regulatory circuits and what input data sets do they accept?

Answer 1

[Jelena Aleksic]

In general, Cytoscape is a common tool for analysing networks (including transcriptional ones). The most basic input is just a table of paired interactions (columns listing: gene A, gene B, type of interaction) that you can then visualise, but there are loads of Cytoscape plug-ins built for particular types of network analysis, and dealing with extra types of data.

However, exactly what type of tool would be appropriate really depends on what sort of data you're reconstructing regulatory circuits from.