POTFUL#

Integrated systems biology pipeline to compare co-expression networks in plants and elucidate differential regulators.#

This is a brife tutorial on POTFUL. It shows off a few of the major file types, as well as sample scripts.

Abstract#

To identify sets of genes that exhibit similar expression characteristics, co-expression networks are constructed from transcriptome datasets that were obtained from plant samples at various stages of growth and development or treated with diverse biotic, abiotic and other environmental stresses. In addition, co-expression network analysis can provide deeper insights into gene regulation when combined with transcriptomics. Coordination and integration of all of these complex networks to deduce gene regulation are major challenges for plant biologists. Python and R have emerged as major tools for managing complex scientific data over the past decade. Here, we described a reproducible protocol POTFUL (Plant c O-expression Transcription Factor regULators), implemented in Python 3, for integrating co-expression and transcription factor-target protein networks to infer gene regulation.