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Fig. 6 | BMC Genomics

Fig. 6

From: A homology-guided, genome-based proteome for improved proteomics in the alloploid Nicotiana benthamiana

Fig. 6

Annotation of the N. benthamiana apoplastic proteome. a Correlation matrix heat map of the log2 transformed LFQ intensity of protein groups in the four biological replicates of apoplastic fluid (AF) and total extract (TE) samples. Biological replicates are clustered on similarity. b A volcano plot is shown plotting log2 fold difference (log2FC) of AF/TE over –log10 BH-adjusted moderated p-values. Proteins with log2FC ≥ 1.5 and p ≤ 0.01 were considered apoplastic, as well as those only found in AF. Conversely, proteins with a log2FC ≤ 1.5 and p ≤ 0.01 were considered intracellular, as well as those found only in TE. c Percentage of proteins in each fraction annotated with biological process-associated GO-SLIM terms. d Percentage of proteins in each fraction annotated with molecular function-associated GO-SLIM terms. c and d GO-SLIM annotations are shown when significantly enriched or depleted (BH-adjusted hypergeometric test, p < 0.05) in at least one of the fractions (AF, TE, or both). Each bubble indicates the percentage of genes containing that specific GO-SLIM annotation in that compartment. Colours indicate whether the GO-SLIM annotations are enriched or depleted in that fraction (p < 0.05, n.s., non-significant).

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