Figure 4

Gallery of Gaggle Genome Browser visualizations. (1) H. salinarum growth series showing 14 tracks of strand sensitive tiling array data taken as a time series during growth. The track nearest the horizontal axis shows reference RNA, while the remainder of the tracks are log ratios relative to the reference. Segmentation, overlaid on the reference RNA in red, computationally delimits transcriptional units. Ratios are also overlaid with segmentation, using red to indicate increased expression and green for decreased expression relative to the reference for that segment. This view shows about 200 thousand features out of 7.25 million in the whole dataset. (2) A view supporting curated annotation of transcriptional start and termination sites. Heatmaps are used to represent tiling array data relative to the reference condition, shown with blue circles overlaid with segmentation in red. Computed boundaries of transcription are drawn as dashed verticals with supporting statistics shown in brown and green along the outer edge. Blue blocks show PFAM domains. Dark blue bars show computationally predicted operons. (3) A comparison of array platforms. Data from different tiling array platforms is compared to spotted expression arrays. On the outer edge, we overlay all time points from both replicates giving some idea about the distribution of values at each point. (4) MeDiChI profiles and predicted binding sites overlay multiple replicates of ChIP-chip data for several transcription factors, showing TF binding sites in relation to genes and transcription data.