(1) Accessions input box. Enter gene accessions for chromatin visualization.
If the Chromatin Trend tool is selected (as in this example) an unlimited number of accessions can be entered.
Use either standard yeast gene names (e.g. YOR234C) or common gene names (e.g. PHO5), and separate
each name with a return. For the purposes of this tutorial, we will visualize the average nucleosome organization of 92 ribosomal protein genes.
(2) Visualization type menu. Select Chromatin Trend or Promoter Display visualization tools.
(3) Nucleosome Data Set #1. Select the first Nucleosome data set for visualization. Options include nucleosome positions mapped in normal growing cells (30C in YPD media) using MNase-microarray methodology (normal MNase-microarray), nucleosome positions in normal cells mapped using MNase-seq methodology (normal MNase-seq), and nucleosome positions mapped in heat shocked cells (39C for 15 minutes) using MNase-seq methodology (heat-shock MNase-seq). In this example, the normal MNase-microarray data set has been selected.
(4) Nucleosome Data Set #2. Select the second Nucleosome data set for visualization. Note that at least one, and a maximum of two, nucleosome data sets may be selected. In this example, a second nucleosome data set was not selected.
(5) Promoter size menu Select the maximum size of the promoter (in bp upstream) and whether to truncate the promoter when it overlaps with the next gene upstream (check box to truncate promoters that overlap with upstream genes). For this tutorial we have selected a 1000 bp maximum promoter length and to truncate promoters that overlap with upstream genes.
(6) Use Nucleosome Positioning Scores Option. If this option is selected, then the nucleosome positioning (i.e. fuzziness) score is used to calculate the average nucleosome positioning. If this option is not selected, then each nucleosome is assigned an arbitrary score of 1.
(7) Calculate Correlation Coefficient Option. If this option is selected, then Ceres will calculate the correlation coefficient describing the similarity of the nucleosome profiles of the selected genes. Note that this option is slow, and should not be selected if more than ~150 accessions are being analyzed.
After adding the gene accession names and selecting the appropriate display options, click the display button to visualize the promoter sequences.