3.6.2 MEME-Suite
Similar to Cistome, tools within MEME-suite [38] can search a
collection of genes for enriched sequences, or scan sequences of
interest to find matches to known motifs. Unlike Cistome, users
can take advantage of the DAP-seq data set from the Ecker Lab,
which has identified transcription factor binding sites for hundreds
of transcription factors [39]. Users can also perform de novo motif
enrichment to discover new motifs independent of a motif database. Here, we will discuss how to utilize two tools from MEMEsuite: FIMO [40] and AME [41]. FIMO (Find Individual Motif
Occurrences) scans one or more sequences for individual matches
to each motif in a database (see Supplemental Data from [39]).
AME (Analysis of Motif Enrichment) searches for known motifs
that are enriched across input sequences compared to control
sequences.
Fig. 10 Partial output of a Cistome query that represents the overrepresented regulatory elements mapped
onto the promoters of ABI3 developmentally coexpressed genes. Blue symbols represent the ERD1 motif. The
G-Box motif is also returned as being significantly overrepresented in this set of genes
Arabidopsis Bioinformatics
49
Similar to Cistome, tools within MEME-suite [38] can search a
collection of genes for enriched sequences, or scan sequences of
interest to find matches to known motifs. Unlike Cistome, users
can take advantage of the DAP-seq data set from the Ecker Lab,
which has identified transcription factor binding sites for hundreds
of transcription factors [39]. Users can also perform de novo motif
enrichment to discover new motifs independent of a motif database. Here, we will discuss how to utilize two tools from MEMEsuite: FIMO [40] and AME [41]. FIMO (Find Individual Motif
Occurrences) scans one or more sequences for individual matches
to each motif in a database (see Supplemental Data from [39]).
AME (Analysis of Motif Enrichment) searches for known motifs
that are enriched across input sequences compared to control
sequences.
Fig. 10 Partial output of a Cistome query that represents the overrepresented regulatory elements mapped
onto the promoters of ABI3 developmentally coexpressed genes. Blue symbols represent the ERD1 motif. The
G-Box motif is also returned as being significantly overrepresented in this set of genes
Arabidopsis Bioinformatics
49