Table 1.
Abbreviations used for 16 sample types.
Figure 1.
Gene Set Enrichment Analysis based on sparse principal component analysis (sPCA).
GO terms representing differentially regulated functional classes of genes in at least two of the four tissues (p<0.05). Color values correspond to p-values, as indicated by color bars. Total genes in each gene set (more than ten genes) are given in parentheses. Each column represents one of four tissues: IF, immature fruits; MF, mature fruits; YL, young leaves; ML, mature leaves. Complete GSEA results, including sets with <10 genes, and enriched in one tissue only, are given in Dataset S2.
Table 2.
Differentially regulated* pathways in response to HLB disease.
Figure 2.
HLB-regulation of photosynthesis and carbohydrate metabolism.
Overview of changes induced by HLB in the expression of genes affecting photosynthesis and small carbohydrate metabolism (AH vs. SY samples; see Table 1 for a key to abbreviations for sample types).
Figure 3.
HLB-induced modulation of hormone-mediated immune responses.
Four AH vs. SY tissues were analyzed. Regulatory interactions between pathways [30] are shown. See Table 1 for a key to abbreviations for sample types.
Figure 4.
Predicted protein-protein interaction networks of Citrus responses to HLB disease.
Four citrus tissues were analyzed using the dataset of HLB-regulated genes in SY versus AH samples based on an Arabidopsis knowledgebase. HLB-regulated proteins are represented by the larger nodes. (Fold ratio >1 or <−1). See Table 1 for a key to abbreviations for sample types.
Figure 5.
Transcriptional regulation of fruit and leaf metabolism and sugar transport during HLB disease.
qRT-PCR data compared AH and SY tissues. White triangles within filled squares indicate up- and down-regulated genes. Arrows pointing up and down likewise indicate increased and decreased metabolite concentration. In each bar graph, AH appears on the right, and SY on the left, where vertical axis units are relative ratios of the test gene and housekeeping gene abundance.
Table 3.
Numbers of genes with non-zero coefficients in each tissue type in Sparse Principal Component Analysis.