Each "motif probability curve" shows the (estimated) probability of the best match to a given motif occurring at a given position in the input sequences. This estimated probability is based only on sequences that contain at least one match with than the threshold defined for this motif, and is the maximum likelihood estimate of the conditional probability shown below.

Points (X,Y) on the plot are:
  Y = Pr(best match occurs at position X | sequence contains a match)

Note: The plots are smoothed according to the function selected from the "Smoothing" menu on the right. Setting the smoothing window size to 1 turns off smoothing.

If a negative dataset has been supplied then two curves are drawn for each motif, one for each dataset. The distribution of the motif in the primary dataset is plotted with a single unbroken curve, whereas the distribution in the negative dataset is plotted with a dashed curve.

This shows a listing of all motifs currently plotted on the graph.

The color used to plot a motif can be changed by clicking on the color swatch next to the motif you want to change, followed by clicking on the color swatch you wish to swap it with.

These are extra colors you may use for plotting motifs.

Click on the color swatch next to one of the above motifs, then click on one of these "unused color" swatches to change the color of the motif's plot.

These options change the display of the graph.

Smoothing:

Allows selection of the smoothing function applied to the graph.

The weighted moving average option uses weights shaped as an isosceles triangle where the central point (or points in an even sized window) get the maximum weight.

The moving average simply weights all points in the smoothing window equally.

Note: Setting the smoothing window size to 1 turns off smoothing.

Window

The window size used to smooth the graph. The larger the smoothing window size, the smoother the graph, at the cost of hiding detail.

Below a smoothing window size of 10, thinner lines are used on the graph to allow more detail to be visible.

Note: Remember to press "return" or "enter" after changing the number in the input box in order to see the effect of the new smoothing window size.

Legend

Choose to display/disable the on-graph legend. The legend can be moved by clicking on the graph.

Negative Sequences

Choose whether to plot the motif probability curve(s) for the negative sequences (if provided). The curve(s) are plotted as dashed lines, using the same color as the corresponding curve for the positive sequences.

Zoom

Drag a range on the graph to zoom into that section. Clicking "Undo Zoom" will return the view to the previously displayed part of the graph and clicking "Center on 0" will move the view so 0 is in the center.

Download EPS

Download the graph that you are currently viewing as an encapsulated postscript (EPS) image. EPS images are scalable making them suitable for publication.

List only enriched motifs that meet the selected filter criteria below.

Selected motifs are always listed; deselect all motifs first by clicking on the "X" above the color swatches if you wish to filter all motifs.

To filter on "ID" or "Name", you can enter any Javascript regular expression pattern. See here for documentation on Javascript regular expression patterns.

Sorting is applied after filtering where possible (the exception being the "Top" filter) so the filters applied will affect the sort. You can choose the motif sorting feature using the "Motifs:" menu.

If CentriMo is searching for locally enriched regions (not just centrally enriched regions), then multiple regions may be found per motif, and the "Regions:" menu will also be displayed. In this case, CentriMo first sorts all regions using the feature shown in the "Regions:" menu, and then it sorts the highest-ranked region of each motif according to the feature shown in the "Motifs:" menu.

Unless you check the box next to the "Regions:" menu, it will automatically show the same feature as the "Motifs:" menu (or "E-value" if a motif-only feature is chosen in the "Motifs:" menu).

Note:The motif p-value shown in the plot legend will always be for the region with the lowest p-value, and therefore may not match the value shown in the table "p-value" column when the "Regions:" menu is not set to "p-value".

The expected number motifs that would have least one region as comparatively enriched for best matches to the motif as the reported region in the positive sequences compared with the negative sequences.

The Fisher E-value is the (one-sided) p-value of the one-sided Fisher's exact test that at least as many best matches in the region in the positive sequences that contain at least one match, multiplied by the number of motifs in the input database(s). The Fisher's exact test p-value is corrected for the number of regions and score thresholds tested ("Multiple Tests").

Fisher's exact test assumes that the probability that the best match (if any) falls into a given region is the same for all positive and negative sequences.

The Matthew's Correlation Coefficient (MCC) gives a measure of the ability of the motif to discriminate the positive sequences from the negative sequences:

MCC = [TP*TN - FP*FN] / [(TP + FP) * (TP + FN) * (TN + FP) * (TN + FN)]

TP is the number of positive sequences with a best match in the reported region,

FP is the number of negative sequences with a best match in the reported region,

TN is the number of negative sequences without a best match in the reported region, and

FN is the number of positive sequences without a best match in the reported region.

MCC ranges from -1 to +1, where a +1 result indicates that the occurrence of the best match to the motif in the reported region perfectly discriminates positive sequences from negative sequences.

The number of negative sequences where the best match to the motif falls in the reported region. This value is rounded but the underlying value may contain fractional counts.

Note: This number may be less than the number of negative have a best match in the region. The reason for this is that a sequence may have many matches that score equally best. If n matches have the best score in a sequence, 1/n is added to the appropriate bin for each match.

The number of sequences containing a match to the motif the threshold ("Score Threshold").

This is the threshold () for determining if a sequence contains a match to this motif.

The number of negative sequences containing a match to the motif above the score threshold. When score optimization is enabled the score threshold may be raised higher than the minimum.

The probability that any tested region in the negative sequences would be as enriched for best matches to this motif according to the Binomial test.

Use the filter to display only motifs differentially enriched in both datasets (low p-value and high negative p-value).

The maximum probability that the best match occurs at any single sequence position. If the smoothing window size ("Window:", to right of graph) is set to "1", then this is value is the maximum value of the match-probability curve.

Concentration is defined as the total probability of all the positions in the central region whose width is the same as the size of the "smoothing window". You can change the size of the smoothing window using the "Window:" input field in the Graph options section, above. (A value of "NaN" indicates that the smoothing window size is too large for the motif.)

The "concentration" of the motif sites in the central window can somtimes be more informative than the E-value. For example, in some ChIP-seq datasets, motifs for cofactors show more significant enrichment overall (smaller E-value), but are less concentrated in a small (20 to 50bp) window than the motif for the ChIP-ed transcription factor. In such cases, you may wish to sort the motifs by Concentration, using the Sort menu, below.

Location of the center of the most enriched region.

The text box lists the sequence identifiers for sequences that all the selected motifs.

The "Intersection" subheading gives the number of identifiers in the text box and their percentage out of the total number of input sequences.

The "Union" subheading lists the number and percentage of sequences that have at least one of their best matches in the most significant region of any of the selected motifs and their percentage out of the total number of input sequences.

Note that the number of sequences with a match to a given motif in its best region may be larger than the value of "Region Matches". This is because a sequence may have multiple equally best matches and in that case a fractional match count is assigned to each of them when "Region Matches" is computed.

When more than one significant, non-overlapping region is found, they can be shown (and hidden again) by clicking the arrow.

By default the regions are sorted by E-value, but this can be changed by the menu on the right of the page.

Sequence position where the (unsmoothed) match-probability curve for this motif attains its maximum. Set the smoothing window size ("Window:", to right of graph) to "1" to see the unsmoothed match probability curve.