Growth phase dependency of mutability in NAP-bound sequence.

<p>The top left panel shows schematically when NAP binding was assayed by Chip-Seq during the <i>E. coli</i> growth cycle. The remaining panels depict mutability at 4-fold synonymous sites as a function of the binding of a specific NAP (or of all NAPs combined) at a specific stage during the growth cycle. The colour coding corresponds to the colours of the growth phase labels in the top left panel. Note that mutability estimates for a certain growth phase do not only include regions that are exclusively bound during that phase but also include regions that are bound at several stages during the growth cycle.</p

Mutability at 5-methylcytosine deamination hotspots.

<p>C∶G to T∶A mutability at the second cytosine in CCWGG motifs and CCWHH control motifs (expressed as changes per context at risk) for sequence bound by a specific NAP (either H-NS, IhfA, or IhfB) either exclusively early (light green) or exclusively late (dark green) or never (blue) bound by any of the NAPs considered (including Fis).</p

Growth phase-specifically bound sequence reveals time-dependent effects of NAP binding on mutability.

<p>Left-hand panels: Mutability as a function of H-NS, IhfA, or IhfB occupancy for all possible transitions and transversions. Light green: sequence bound by the focal protein during mid- and/or late exponential phase but not later. Dark green: sequence bound by the focal protein during transition to stationary and/or stationary phase but not earlier. Blue: sequence not bound by the focal NAP throughout growth. Right-hand panels provide odds ratios along with 95% confidence intervals, where values in excess of 1 indicate higher mutability in exclusively early- versus exclusively late-bound sequence. Note that very few genomic regions are bound exclusively early (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002846#pcbi.1002846.s010" target="_blank">Table S3</a>). This applies to H-NS in particular so that odds ratio estimates are correspondingly noisy.</p

The “Interactive graph” view of REVIGO.

<p>Bubble color indicates the user-provided <i>p</i>-value; bubble size indicates the frequency of the GO term in the underlying GOA database. Highly similar GO terms are linked by edges in the graph, where the line width indicates the degree of similarity. The initial placement of the nodes is determined by a ‘force-directed’ layout algorithm that aims to keep the more similar nodes closer together, but the placement may later be adjusted by the user.</p

REVIGO's “Table” view of seven gene functional categories co-expressed with the human transcription factor ZNF417; data from [<b>14</b>].

<p>“Frequency” is the percentage of human proteins in UniProt which were annotated with a GO term in the GOA database, i.e. a higher frequency denotes a more general term. Cluster representatives are given in black letters and other cluster members are in gray italics and indented. The seven terms are subdivided into four clusters, two of which contain a single term. The ‘pin’ column can be used to manually override the choice of cluster representative.</p

The “Tag Cloud” view of REVIGO.

<p>All displayed words are overrepresented in the descriptions of the GO terms in the user-supplied list, with larger and darker letters signifying stronger overrepresentation. Underrepresented keywords are not displayed in the Tag Cloud.</p

The “TreeMap” view of REVIGO.

<p>Each rectangle is a single cluster representative. The representatives are joined into ‘superclusters’ of loosely related terms, visualized with different colors. Size of the rectangles may be adjusted to reflect either the <i>p</i>-value, or the frequency of the GO term in the underlying GOA database.</p