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. 2022 Jan 29;11(2):219. doi: 10.3390/biology11020219

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© 2022 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Differences in transcription factor (TF) cooperation networks found by the PC-TraFF algorithm for (A) ileum 1 dpi, (B) ileum 3 dpi, (C) lung 1 dpi and (D) lung 3 dpi with HPAIV H5N1. The difference in nodes in the networks of duck and chicken is denoted by the set difference sign (∖). The nodes are labeled by the PWM names representing TFs, as given by TRANSFAC [44]. They follow the structure V$factorname_version, where “V$” indicates that the PWM originates from a vertebrate TF, factorname specifies the name of the corresponding TF, and version is specified to uniquely identify the PWM. The networks were visualized with Cytoscape [74]. Full size image is provided in Figure S3.