“ARABIDOPSIS (A. thaliana) DNA.” Under the second
dropdown menu, select “DAP motifs [39].”
5. Under the “Select the sequence scoring method” drop down
menu, select “Average odds score.”
6. Under the “Select the motif enrichment test” drop down
menu, select “Fisher’s exact test.”
7. Now, enter in job details, such as your email address and job
description describing the AME analysis you are performing.
Similar to FIMO, this step will take at least an hour to run on
the MEME-suite server, so plan accordingly.
8. When the job is done, you should receive an email with a link to
your results. Click the link and you will be taken to an output
page that has the following links: AME HTML output, AME
TSV output, AME true- and false-positive sequences, and
Uploaded Sequences. For future data analysis, download the
TSV file. If you open this TSV file, you will see that for each
motif that was found to be enriched across the input sequences,
information such as the motif consensus sequence, p-value,
adjusted p-value, as well as E-value is supplied. Additional
statistical information is also reported, such as “TP thresh,”
which the optimal score threshold for determining whether a
given sequence is classified as positive for a motif. “TP (%)”
describes the percentage of input sequences that are later determined to contain a given motif. Finally, “FP (%)” is the percentage of control sequences (in this example, the shuffled
input sequences) that were also found to be matches to a
given motif.
9. Click “HTML output.” You will be taken to a page displaying
visual information about the analysis that you performed with
AME. Specifically, you can observe the motif logo plots for
their DAP-seq binding sites. The additional information displayed here is the same TSV that was previously downloaded
(see Fig. 12).
10. At the top of page, click on “Positive sequences for each
motif.” A TSV file containing which input sequences were
found to matches to the motifs in the database. We can see
that among the top ten most significantly enriched motifs,
there are several abscisic acid responsive transcription factors
listed: ABF2, ABI5, and AREB3. It would perhaps be interesting to use FIMO to see where these transcription factors bind
in the upstream sequences of our coexpressed genes.
3.6.3 ePlant Promoter
Analysis
The ePlant website integrates several essential tools for plant biology research. With only a few mouse clicks the user can examine
polymorphisms, visualize gene expression in the whole plant
and/or in different tissues, determine the subcellular localization
52
G. Alex Mason et al.
dropdown menu, select “DAP motifs [39].”
5. Under the “Select the sequence scoring method” drop down
menu, select “Average odds score.”
6. Under the “Select the motif enrichment test” drop down
menu, select “Fisher’s exact test.”
7. Now, enter in job details, such as your email address and job
description describing the AME analysis you are performing.
Similar to FIMO, this step will take at least an hour to run on
the MEME-suite server, so plan accordingly.
8. When the job is done, you should receive an email with a link to
your results. Click the link and you will be taken to an output
page that has the following links: AME HTML output, AME
TSV output, AME true- and false-positive sequences, and
Uploaded Sequences. For future data analysis, download the
TSV file. If you open this TSV file, you will see that for each
motif that was found to be enriched across the input sequences,
information such as the motif consensus sequence, p-value,
adjusted p-value, as well as E-value is supplied. Additional
statistical information is also reported, such as “TP thresh,”
which the optimal score threshold for determining whether a
given sequence is classified as positive for a motif. “TP (%)”
describes the percentage of input sequences that are later determined to contain a given motif. Finally, “FP (%)” is the percentage of control sequences (in this example, the shuffled
input sequences) that were also found to be matches to a
given motif.
9. Click “HTML output.” You will be taken to a page displaying
visual information about the analysis that you performed with
AME. Specifically, you can observe the motif logo plots for
their DAP-seq binding sites. The additional information displayed here is the same TSV that was previously downloaded
(see Fig. 12).
10. At the top of page, click on “Positive sequences for each
motif.” A TSV file containing which input sequences were
found to matches to the motifs in the database. We can see
that among the top ten most significantly enriched motifs,
there are several abscisic acid responsive transcription factors
listed: ABF2, ABI5, and AREB3. It would perhaps be interesting to use FIMO to see where these transcription factors bind
in the upstream sequences of our coexpressed genes.
3.6.3 ePlant Promoter
Analysis
The ePlant website integrates several essential tools for plant biology research. With only a few mouse clicks the user can examine
polymorphisms, visualize gene expression in the whole plant
and/or in different tissues, determine the subcellular localization
52
G. Alex Mason et al.