with the final bar on the right being the category used for
grouping. A gene will appear in this table as often as the
number of bars in its bar code. Mousing over a particular bar
will provide information on the actual GO term.
3.8 Pathway
Visualization
One of the biggest challenges working with large-scale data sets is
to represent the information in a comprehensive manner. This is
particularly relevant in the context of metabolic pathways. If a series
of enzymes in a pathway is upregulated or downregulated, there is a
greater chance that the metabolism of the compounds associated
with this pathway will be perturbed accordingly. Pathway visualization tools were generated to integrate and analyze data from largescale experiments and place that information in an easy-to-interpret
metabolic context. In this section we will introduce two different
visualization tools used to describe a wide set of Arabidopsis metabolic pathways.
3.8.1 AraCyc
AraCyC 8.0 [55] is the most comprehensive Arabidopsis-specific
metabolic database (see Note 21). We can use their tools to visualize individual metabolic pathways, to view the complete metabolic
map of Arabidopsis, or to predict metabolic pathways from a list of
genes. We will demonstrate how to use these three options to
characterize the role of ABI3 as it pertains to plant metabolism.
As ABI3 is highly expressed after treatment with abscisic acid
(ABA), we may be interested in learning more about genes that
function to synthesize ABA.
1. Go to http://www.plantcyc.org/.
2. In the search box write the name (or a keyword) of the pathway
in which you are interested. In our case we will write “Abscisic.” Then choose AraCyc as the metabolic database from the
dropdown. Click the magnifying glass icon to search.
3. The search results contain a window with a list of pathways,
proteins, compounds and reactions that match with our word.
We just need to click on the one we want to explore, in our case
“abscisic acid biosynthesis” (see Fig. 17).
4. AraCyC shows a diagram with the enzymes (orange), compounds (red), genes (purple) and related pathways (green) of
the Abscisic Acid biosynthesis pathway. If we click on “more
detail” the molecular structures of the compounds appear on
the diagram. Below the diagram, we can find information
about the chromosomal localization of the genes in the pathway, a brief description of the biological context of the pathway,
and the references AraCyc used to generate the pathway.
5. To get information about the enzymatic reaction in which the
gene is involved, click on the enzyme name (not the AGI ID).
This will take you to a new window with more information. For
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G. Alex Mason et al.
grouping. A gene will appear in this table as often as the
number of bars in its bar code. Mousing over a particular bar
will provide information on the actual GO term.
3.8 Pathway
Visualization
One of the biggest challenges working with large-scale data sets is
to represent the information in a comprehensive manner. This is
particularly relevant in the context of metabolic pathways. If a series
of enzymes in a pathway is upregulated or downregulated, there is a
greater chance that the metabolism of the compounds associated
with this pathway will be perturbed accordingly. Pathway visualization tools were generated to integrate and analyze data from largescale experiments and place that information in an easy-to-interpret
metabolic context. In this section we will introduce two different
visualization tools used to describe a wide set of Arabidopsis metabolic pathways.
3.8.1 AraCyc
AraCyC 8.0 [55] is the most comprehensive Arabidopsis-specific
metabolic database (see Note 21). We can use their tools to visualize individual metabolic pathways, to view the complete metabolic
map of Arabidopsis, or to predict metabolic pathways from a list of
genes. We will demonstrate how to use these three options to
characterize the role of ABI3 as it pertains to plant metabolism.
As ABI3 is highly expressed after treatment with abscisic acid
(ABA), we may be interested in learning more about genes that
function to synthesize ABA.
1. Go to http://www.plantcyc.org/.
2. In the search box write the name (or a keyword) of the pathway
in which you are interested. In our case we will write “Abscisic.” Then choose AraCyc as the metabolic database from the
dropdown. Click the magnifying glass icon to search.
3. The search results contain a window with a list of pathways,
proteins, compounds and reactions that match with our word.
We just need to click on the one we want to explore, in our case
“abscisic acid biosynthesis” (see Fig. 17).
4. AraCyC shows a diagram with the enzymes (orange), compounds (red), genes (purple) and related pathways (green) of
the Abscisic Acid biosynthesis pathway. If we click on “more
detail” the molecular structures of the compounds appear on
the diagram. Below the diagram, we can find information
about the chromosomal localization of the genes in the pathway, a brief description of the biological context of the pathway,
and the references AraCyc used to generate the pathway.
5. To get information about the enzymatic reaction in which the
gene is involved, click on the enzyme name (not the AGI ID).
This will take you to a new window with more information. For
60
G. Alex Mason et al.