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The files “homerMotifs.motifs*” are the files that contain information of the motifs

found by the de novo motif discovery method, separated by motif length (“*” simply rep-

resents an integer for the length of the motif sequence). The motif information includes the

sequence, statistics, and PWM.

The file “homerMotifs.all.motifs” contains the information of all motifs found by the

de novo method. It is the concatenated file made up of all the “homerMotifs.motifs*” files.

The file “motifFindingParameters.txt” contains the command line used to execute the

program for the motif discovery.

The file “knownResults.txt” contains the statistics about known motif enrichment,

including motif name, consensus, p-value, Log p-value, q-value (Benjamini), number of

target sequences with motif, percentage of target sequences with motif, number of back-

ground sequences with motif, and the percentage of background sequences with motif.

The file “seq.autonorm.tsv” contains autonormalization statistics for the oligo.

The files “homerResults.html” and “knownResults.html” contain the output of de novo

motif finding and known motif finding, respectively. These HTML files can be displayed

on the Internet browser or using Firefox.

firefox homerResults.html knownResults.html

Figure 6.21 shows the motifs (logos and statistics) found by the de novo method using

“findMotifs.pl”. The motifs are ordered by the p-value. The significant motifs must have

very small p-value. Each motif has a link to the motif file.

The PWM motif discovery methods use prior information about the binding or inter-

action sites, obtained via laboratory means. Motif information are stored in a PWM file

format that describes the probability of finding the respective nucleotides A, C, G, and T

on each position of a motif. The word or PWM search method is used only to detect known

binding sites of transcription factors. PWM files of known motifs are used to scan windows

FIGURE 6.21  The motifs found by HOMER.