the genes in the ‘‘overlap’’ category were bound, while those in the ‘‘new’’ down-regulated category were not, indicating that the latter category includes more secondary targets indirectly regulated by Zld. (DOC) Table S2 Differential expression of blastoderm genes in wild- type and zld2 embryos. Selected genes (CG number and symbol) involved in early developmental processes are listed in columns 1 and 2. BD denotes whether a gene is associated (+) or not (2) with Zld-bound regions within 2 kb of the TSS, or within an intron (+*). Gene expression (Affymetrix) and tiling (NimbleGen) profiles of 1–2 hr and 2–3 hr wild-type embryos were compared to that of zld2. Genes with a fold change (FC: wt/zld2, see Materials and Methods) $2 and a p,0.05 were considered significantly down- regulated (FC in red); genes with a fold change #0.5 and a p,0.05 were considered significantly up-regulated (FC in blue). 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Mol Cell Biol 26: 3446–3454. PLoS Genetics | www.plosgenetics.org 15 October 2011 | Volume 7 | Issue 10 | e1002339