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. 2016 Dec 21;6:39709. doi: 10.1038/srep39709

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Copyright © 2016, The Author(s)

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

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The method uses gene expression values and compares two conditions (A and B). However, in this case all the samples in the (B) condition are used to produce an average expression value for any of the genes in this condition (m vector). Then, each sample in the (A) condition (v_c) can be compared to the average expression in the (B) condition and a rank of fold change (F_cg) is generated for each sample. Then, this ranking is used in the same way that the rank of differential expression was used in Fig. 6 to find differentially activated TFs in samples from the condition (A) with respect to the average (B) condition. Is samples are paired the F_cg value can be derived from the direct comparison between them.