Figure 5
From: Bioinformatic identification of novel putative photoreceptor specific cis-elements
(A) Occurrences of a sample ambiguous motif (triangles) analyzed using position cluster discovery. The horizontal axis represents position relative to the putative transcription start site. The vertical position of occurrences was offset to ease viewing. Position clusters (ovals) were identified using agglomerative hierarchical clustering for all occurrences of each motif in the 2 kbp upstream region identified. Clusters with occurrences in the first 400 bp relative to the transcription start site were evaluated for cell-specificity. In this case, the cluster of occurrences nearest the transcription start site is cone-enriched. A second cluster between -250 and -500 is entirely ambiguous. The numbers kr, kc, and kn reflect the number of rod, cone, and background promoters that contain the motif. (B-C) Identification of cell-specific motifs among position-enriched clusters by statistical annotation. The vertical and horizontal axes plot the fraction of rod (B) or cone (C) promoters against the total number of promoters that contain at least one occurrence of a putative motif. Colors are assigned by the number of motifs with a given fraction (log-10 scale). The shaded region represents groups chosen using a p < 0.005 cutoff threshold.