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bioRxiv · 10.1101/2020.05.19.104935

Co-expression signatures of combinatorial gene regulation

Gomez-Cano, F.·Qian, X.·Shiu, S.-H.·Krishnan, A.·Grotewold, E.
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Abstract

Gene co-expression analyses provide a powerful tool to determine gene associations. The interaction of transcription factors (TFs) with their target genes is an essential step in gene regulation, yet to what extent TFs-target gene associations are recovered in co-expression studies remains unclear. Using the wealth of data available for Arabidopsis, we show here that protein-DNA interactions are overall poor indicators of TF-target co-expression, yet the inclusion of TF-TF interaction information significantly enhance co-expression signals. These results highlight the impact of combinatorial gene control on such gene association networks. We integrated this information to predict higher-order regulatory complexes, which are difficult to identify experimentally. We demonstrate that genes strongly co-expressed with a TF are also enriched in indirect targets. Our results have significant implications on the empirical understanding of complex gene regulatory networks and transcription factor function, and the significance of co-expression from the perspective of protein-protein and protein-DNA interactions.

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Gomez-Cano, F., Qian, X., Shiu, S.-H., Krishnan, A., Grotewold, E.. 2020-05-22. Co-expression signatures of combinatorial gene regulation. https://doi.org/10.1101/2020.05.19.104935

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