Fig. 2.

Sample of a MochiView screenshot illustrating concepts relating to the analysis of ChIP-chip data. Data in this figure is from a ChIP-chip experiment of C. albicans Efg1, a regulator of white-opaque switching, in the opaque cell type. ChIP-chip data for Efg1 (blue, A) and an Efg1 delete control (grey, B) are shown. Open reading frames are represented by yellow boxes (C), lighter yellow represents the untranslated region (D), genes above the bold line are transcribed in the sense direction and genes below the bold line are transcribed in the antisense direction. The x-axis represents ORF chromosomal locations and the y-axis represents the ChIP-chip enrichment value (log₂). A lower track illustrates 500 bp peaks of Efg1 binding (blue boxes, E) and intergenic regions bound by Efg1 (light blue boxes, F) as well as 500 bp Efg1 peaks that do not fall in an intergenic region and would normally be excluded from further analysis (dark blue boxes, G). High-scoring instances of the Efg1 DNA-binding motif (maximum possible score 4.17) is indicated (H). The plot also contains data from a microarray analysis of an opaque efg1 deletion strain versus wildtype opaque cells; values are on a log 2 scale (I) with downregulated genes in green and upregulated genes in red, color intensity represents differences from wild type (with darker colors having greater differences). The data for Chip-chip, Efg1 motif, and Efg1 delete microarray analysis was taken from Hernday et al. [9]. Plots were constructed using MochiView 1.46, see Homman et al. [11]