Global and phenotype-specific AMD disease modules. (a, b) Disease-associated genes with permuted P-value < 0.1 and fold difference ≥ 1.5 were clustered based on their significance score (see Materials and methods), and the results are displayed as heat maps for RPE-choroid (a) and retina (b). Columns represent each disease phenotype, macula (Mac) and/or extramacula (XMac), and rows represent unique genes/probes (gene symbols/Agilent ID). Global includes all AMD/pre-AMD phenotype classifications, and MD is composed of both MD1 and MD2 donor samples. GA and CNV disease classes include GA/CNV donor samples. Disease modules are separated by horizontal lines and labeled by higher or lower expression in one or more AMD/pre-AMD phenotypes (for example, 'MD2 Up', 'GA Down') compared to age-matched normal donor samples. Global Up*/Global Down* disease modules enlarged on the right highlight individual genes with significant differential expression in both macular and extramacular donor samples; for the entire list of Global Up/Down genes, see Figures S7 and S8 in Additional file 1 and Table S3 in Additional file 5. Immunoglobulin probes are averaged to conserve space, as described in Materials and methods.