and have curved lines indicating interactions with other proteins. As we see in Fig. 13, ABI3 has a total of 76 protein-DNA
interactions, all of which are predicted, as denoted by the gray
dashed lines.
3.6.4 TAIR Motif Analysis
Cistome analyzes promoters for overrepresented previously validated or characterized regulatory elements. Cistome also provides
access to 5 other prediction programs. The Motif Analysis algorithm from TAIR provides an alternate approach by searching for
overrepresented 6-mer oligos in upstream regions of genes.
1. Go to http://www.arabidopsis.org/tools/bulk/motiffinder.
2. Add your list of genes by typing the AGI ID or the sequences in
Fasta format. Here we will use the list of genes in Supplementary Table S1.
3. Indicate the length of the regulatory sequence that will be
included in the analysis (e.g., 3000bp) and select the output
file type (e.g., HTML). Click Submit.
4. Motif Analysis from TAIR identifies statistically overrepresented 6-mer oligos occurring in 3 of more sequences in the
gene set. The overrepresented 6-mers are sorted by p-value
determined by comparing against a binomial distribution, and
genes/promoters with a particular sequence 6-mer sequence
Fig. 13 ePlant Interaction Viewer output for ABI3. There are 76 FIMO-predicted DNA interactions for ABI3, as
denoted by the gray dashed lines to the 5 chromosome boxes
54
G. Alex Mason et al.
interactions, all of which are predicted, as denoted by the gray
dashed lines.
3.6.4 TAIR Motif Analysis
Cistome analyzes promoters for overrepresented previously validated or characterized regulatory elements. Cistome also provides
access to 5 other prediction programs. The Motif Analysis algorithm from TAIR provides an alternate approach by searching for
overrepresented 6-mer oligos in upstream regions of genes.
1. Go to http://www.arabidopsis.org/tools/bulk/motiffinder.
2. Add your list of genes by typing the AGI ID or the sequences in
Fasta format. Here we will use the list of genes in Supplementary Table S1.
3. Indicate the length of the regulatory sequence that will be
included in the analysis (e.g., 3000bp) and select the output
file type (e.g., HTML). Click Submit.
4. Motif Analysis from TAIR identifies statistically overrepresented 6-mer oligos occurring in 3 of more sequences in the
gene set. The overrepresented 6-mers are sorted by p-value
determined by comparing against a binomial distribution, and
genes/promoters with a particular sequence 6-mer sequence
Fig. 13 ePlant Interaction Viewer output for ABI3. There are 76 FIMO-predicted DNA interactions for ABI3, as
denoted by the gray dashed lines to the 5 chromosome boxes
54
G. Alex Mason et al.