1. Go to http://www.genemania.org/.
2. GeneMania integrates data from seven different organisms. In
the top left select the Arabidopsis thaliana icon and add your
gene or list of genes. GeneMania recognizes gene names and
AGI IDs. If GeneMania doesn’t recognizes your query it will
tell you with a yellow speech bubble. We will add ABI3
(At3g24650) and PIF1 (At2g20180 – also called PIL5) in
the second window (one gene per line) to try to predict a
mechanism for why ABI3 expression is downregulated in pif1pif3pif4pif5 quadruple mutant plants.
3. On the left part of the window a network graph visualized
using Cytoscape is displayed with colored edges to indicate
different interaction types between different genes. Brown
indicates predicted interactions, gray indicates coexpression,
dark blue indicates physical interactions, light blue indicates
co-localization, and green indicates genetic interactions. On
the right side of the window, there are four tabs. The “network” tab gives us the option to select the type of interactions
we want to see on the right diagram, e.g., we can check the
physical interactions tab only. It appears that PIL5 could form a
protein complex with ABI3 and At5g61380. There are many
examples by which protein complexes can have autoregulatory
function on one or more of the members of the protein complex [70]. By clicking on the nodes that represent the genes, we
get more details of a gene’s function. For instance, At5g61380
is a two-component response regulator and possesses transcription regulatory activity. The “gene” tab gives a list of interactors with our query proteins, e.g., the DELLA protein interacts
with PIL5/PIF1. It has been described that DELLAs repress
PIF activity and that they are accumulated in the absence of GA
[71, 72]. This could potentially be the mechanism by which
negative crosstalk exists between ABA and GA. The “Functions” tab shows the GO annotation of the genes in the network. We can sort the list by GO annotation name, by the False
Discovery Rate or by Coverage (number of genes in the network with a given function divided by all the genes in the
genome with that function) (see Fig. 26).
4. Above the network diagram there is a bar with more options to
save the data or to play with network graph visualization.
3.11.3 ePlant
The ePlant website [73] 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
of a protein, find its interactors, and view predicted or experimentally determined protein structures.
74
G. Alex Mason et al.
2. GeneMania integrates data from seven different organisms. In
the top left select the Arabidopsis thaliana icon and add your
gene or list of genes. GeneMania recognizes gene names and
AGI IDs. If GeneMania doesn’t recognizes your query it will
tell you with a yellow speech bubble. We will add ABI3
(At3g24650) and PIF1 (At2g20180 – also called PIL5) in
the second window (one gene per line) to try to predict a
mechanism for why ABI3 expression is downregulated in pif1pif3pif4pif5 quadruple mutant plants.
3. On the left part of the window a network graph visualized
using Cytoscape is displayed with colored edges to indicate
different interaction types between different genes. Brown
indicates predicted interactions, gray indicates coexpression,
dark blue indicates physical interactions, light blue indicates
co-localization, and green indicates genetic interactions. On
the right side of the window, there are four tabs. The “network” tab gives us the option to select the type of interactions
we want to see on the right diagram, e.g., we can check the
physical interactions tab only. It appears that PIL5 could form a
protein complex with ABI3 and At5g61380. There are many
examples by which protein complexes can have autoregulatory
function on one or more of the members of the protein complex [70]. By clicking on the nodes that represent the genes, we
get more details of a gene’s function. For instance, At5g61380
is a two-component response regulator and possesses transcription regulatory activity. The “gene” tab gives a list of interactors with our query proteins, e.g., the DELLA protein interacts
with PIL5/PIF1. It has been described that DELLAs repress
PIF activity and that they are accumulated in the absence of GA
[71, 72]. This could potentially be the mechanism by which
negative crosstalk exists between ABA and GA. The “Functions” tab shows the GO annotation of the genes in the network. We can sort the list by GO annotation name, by the False
Discovery Rate or by Coverage (number of genes in the network with a given function divided by all the genes in the
genome with that function) (see Fig. 26).
4. Above the network diagram there is a bar with more options to
save the data or to play with network graph visualization.
3.11.3 ePlant
The ePlant website [73] 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
of a protein, find its interactors, and view predicted or experimentally determined protein structures.
74
G. Alex Mason et al.