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. 2017 Apr 11;114(17):E3563–E3572. doi: 10.1073/pnas.1701952114

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Fig. 5. — Differential expression profiling of WT, stop1, and almt1 revealed a loss of transcriptional response to Pi starvation in the root apex of stop1 and almt1. (A) Venn diagram of differentially expressed genes (DEG) that are up- and down-regulated [−1.5 > logFC(−Pi/Pi) > 1.5; FDR < 0.05] in the root tip of WT, stop1, and almt1 seedlings in response to −Pi conditions. A bar graph illustrating the number of up-regulated and down-regulated transcripts in WT, stop1, and almt1 is presented. (B) Gene ontology (GO) enrichment analysis of overrepresented categories that are activated in the root apex of Pi-deprived WT seedlings. Each circle corresponds to a significantly enriched GO category (P value <0.05; hypergeometric test; Benjamini–Hochberg correction). Color code resembles P value and size resembles the number of genes that are associated with that respective GO category. GO categories that share genes are connected and clustered by the biological process that corresponds to the most significantly enriched category of the cluster. (C) Analysis of DEG by cluster in the root tip of stop1 and almt1. The number of genes that belong to each GO cluster, and are differentially expressed in stop1 and almt1, is presented as a percentage of the number of genes that are differentially expressed in WT (% DEG of WT). (D) Transcriptomic analysis of locally and systemically regulated genes in the root apex of WT, stop1, and almt1 revealed a key role of STOP1 and ALMT1 in the local response to Pi starvation in Arabidopsis. WT, stop1, and almt1 logFC values of genes that are differentially expressed in the root tips of WT seedlings [−1.5 > logFC(−Pi/Pi) > 1.5; FDR < 0.05] in response to −Pi conditions and were reported as PHR1-direct targets (6) and of those that were classified as part of the local or systemic transcriptional response as reported in ref. 5 is represented in a heatmap, respectively. Genes that are differentially expressed in WT root tips and their expression levels in WT, stop1, and almt1 seedlings grown under −Pi conditions are illustrated according to the key.