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. 2015 Dec 17;6:989. doi: 10.3389/fpls.2015.00989

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Copyright © 2015 Howe, Horvath, Dharmawardhana, Priest, Mockler and Strauss.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Relative expression of differentially expressed chromatin-associated genes. Chromatin-associated genes were identified using the Arabidopsis thaliana chromatin database (ChromDB; Gendler et al., 2008). Genes were classified into four groups: up-regulated or down-regulated from paradormancy to endodormancy (A,B), or up-regulated or down-regulated from endodormancy to ecodormancy (C). Within each group, we ranked genes by FDR p-value, and then displayed the top 15 genes for each group if they had a FDR p-value < 0.05. Only four genes were differentially expressed between endodormancy and ecodormancy, and all of these were up-regulated (C). Gene expression values are the means for each month normalized to a mean of zero and a standard deviation equal to the ANOVA RMSE from the analysis of gene expression differences among months. ChromDB is the ChromDB identifier, Populus gene is the P. trichocarpa gene-locus name, and AGI and TAIR10 symbols are the Arabidopsis gene identifiers and gene symbols from the P. trichocarpa v3.0 annotations (http://www.phytozome.net/).