This is the title of the pLogo. By default, the title denotes the foreground (FG) and background (BG) used for the analysis. Titles can be altered (or omitted) within the customize tab at the left of the pLogo.
The y-axis on a pLogo denotes the log-odds binomial probability. By default pLogos are normalized such that the sum of the log-odds probabilities for the largest column is used as the max value for the axis. However, the max value for the y-axis can easily be adjusted in the customize tab to the left of the pLogo. Adjusting the max value can be particularly useful for comparing two or more pLogos side-by-side.
Residues (or nucleotides) in this area of the pLogo are overrepresented in the foreground with respect to the chosen background. Symbols are stacked such that the most statistically significant residues/nucleotides are closest to the x-axis.
The pLogo legend illustrates,
These correspond to the web address and version of the pLogo tool used to create the observed pLogo.
fixed positions are invariant across all sequences used to generate the pLogo, and can be very useful to understand conditional probabilities within a motif. For example, in aligned phosphorylation data, one may want to make the central phosphorylated residue fixed to observe differences in kinase motifs when Ser or Thr are alternatively selected as the central residues. fixed positions in a pLogo are designated by a grey background. Additionally, fixed positions, by their nature, have no underrepresented residues/nucleotides displayed.
Residues/nucleotides can be made fixed (or released from being fixed) simply by clicking on them in the pLogo. It is important to note that at present the pLogo web tool only allows statistically significant residues/nucleotides (those with log-odds values exceeding the p-value threshold) to be made fixed.
This bar represents the p = 0.05 statistical significant threshold following Bonferroni correction. The log-odds value corresponding to this threshold is provided on the y-axis and in the pLogo legend at the bottom left. Since residues/nucleotides are stacked from most to least significant, the red horizontal bar provides a quick method to assess the statistical significance of the most statistically significant residues at each position in a pLogo. The statistical significance (and log-odds value) for all observable residues/nucleotides can be obtained by mousing over them in the pLogo.
Residues/nucleotides in a pLogo are scaled proportional to their log-odds binomial probabilities under the background chosen for the analysis. Thus, the larger a residue/position, the more statistically significant it is. By default, residues are colored according to their physiochemical properties, and can be altered using the customize tab to the left of the pLogo (nucleotides are each given a different color by default).
Mousing over a residue/nucleotide provides various specific statistics including the Bonferroni corrected p-value, corresponding log-odds value, and importantly, the total number of occurrences of the residue/position in the foreground and background data sets. Note that when other residues/nucleotides in a the pLogo have been made fixed, the residue/nucleotide statistics are conditional upon the fixed positions.
These are the position numbers of the pLogo. They can be changed to start at any value (including negative numbers) by altering the “axis” subheading in the customize tab.