of a protein, find its interactors, and view predicted or experimentally determined protein structures. We will focus on the interactors
but let us try a few of the other views first.
1. Go to http://bar.utoronto.ca/eplant.
2. Type the gene name or AGI ID of your gene of interest next
into the input box, at the top left of the page. We will use
At3g24650 for ABI3.
3. Click on the “Plant eFP” or “Cell eFP” to explore expression
levels in the whole plant, in a specific tissue or developmental
stage, or to determine where the protein is localized in the cell
(in the case of ABI3, mostly in the nucleus). Expression levels
are represented from yellow (low) to red (high) in each drawing. Within “Plant eFP Viewers” or “Tissue & Experiment eFP
Viewers,” you can use the toolbar at the top to adjust your
view. Try toggling between “absolute” and “relative” expression levels—“relative” is useful for perturbation type experiments where one sample serves as a control for others that have
been subjected to some sort of stimulus. Additionally, you can
click on “Download Raw Data” in the upper gray toolbar to
download the numerical gene expression information.
4. Next, click on “Interaction viewer” to view interactors of our
gene or gene product. The PDI data used in ePlant comes from
the DAP-seq generated in the Ecker Lab [39] and from Y1H
experiments [42–49], as well as predicted interactions based on
FIMO [40] mapping. DNA elements are displayed as square
Fig. 12 HTML output of an AME analysis with ABI3 developmentally coexpressed genes. Here, transcription
factor motifs that are enriched in the 500-bp upstream region of the input genes (i.e., in their promoters) are
ranked by p-value
Arabidopsis Bioinformatics
53
but let us try a few of the other views first.
1. Go to http://bar.utoronto.ca/eplant.
2. Type the gene name or AGI ID of your gene of interest next
into the input box, at the top left of the page. We will use
At3g24650 for ABI3.
3. Click on the “Plant eFP” or “Cell eFP” to explore expression
levels in the whole plant, in a specific tissue or developmental
stage, or to determine where the protein is localized in the cell
(in the case of ABI3, mostly in the nucleus). Expression levels
are represented from yellow (low) to red (high) in each drawing. Within “Plant eFP Viewers” or “Tissue & Experiment eFP
Viewers,” you can use the toolbar at the top to adjust your
view. Try toggling between “absolute” and “relative” expression levels—“relative” is useful for perturbation type experiments where one sample serves as a control for others that have
been subjected to some sort of stimulus. Additionally, you can
click on “Download Raw Data” in the upper gray toolbar to
download the numerical gene expression information.
4. Next, click on “Interaction viewer” to view interactors of our
gene or gene product. The PDI data used in ePlant comes from
the DAP-seq generated in the Ecker Lab [39] and from Y1H
experiments [42–49], as well as predicted interactions based on
FIMO [40] mapping. DNA elements are displayed as square
Fig. 12 HTML output of an AME analysis with ABI3 developmentally coexpressed genes. Here, transcription
factor motifs that are enriched in the 500-bp upstream region of the input genes (i.e., in their promoters) are
ranked by p-value
Arabidopsis Bioinformatics
53