Expression Source / Select Source dropdown on the top right of
the output screen. After you have chosen the Expression
Source, you can then Select Tissues. The “Source” option allows
you to explore different compendia (the same ones as visible in
the various eFP Browser views described earlier), while the
“Tissues” option allows you to choose which tissue or condition within a given compendium you are interested in using to
retrieve expression level data for painting onto the nodes. In
this case, we will examine the expression levels in Seeds Stage
10 w/o Siliques in the Developmental_Map data source by
selecting these and toggling the Overlay Expression button.
These data are mostly from Schmid et al. [25]. In this case we
see that ABI3 and ABI5 (but not the other interactors) are both
strongly expressed in the seeds at later stages of development,
consistent with their known biological roles. It is possible to
explore the expression levels for the corresponding nodes
(genes) by selecting different data sets and tissues/conditions
to permit you to identify other tissues in which other nodes are
more strongly expressed (e.g., Tissue_specific / Guard Cells no
ABA).
3.11 Integrated Tools
Integrated tools associate data from multiple heterogeneous
sources of genomic data to obtain more accurate predictions.
Most of the bioinformatics tools described in this section integrate
protein and genetic interactions, pathways, coexpression,
co-localization and protein domain similarity and allow the user
generate hypotheses in a rapid and facile manner.
3.11.1 VirtualPlant
VirtualPlant [68] integrates genomic data from different sources
(see Note 24) and provides a set of tools to visualize and analyze
these data. One extremely useful attribute of VirtualPlant is that
data and analyses can be stored on the website.
1. Go to http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/. If
you wish to store your data, click on “Login” to register. The
dark blue navigation bar at the top of the page contains the
different VirtualPlant tools.
2. Click on “Query.” To perform a query, select an option on the
type list (i.e., genes) and add a keyword (e.g., ABI3). The
results are displayed in a table; click on the gene that best
matches your query (i.e., ABI3, At3g24650). VirtualPlant
shows all the information available on the server about our
query, including annotation, gene models, and external links.
For additional data click on the “Gene Family” folder to see
more members of the ABI3VP1 transcription factor family—
the ABI3VP1 family has 11 members.
Arabidopsis Bioinformatics
71
the output screen. After you have chosen the Expression
Source, you can then Select Tissues. The “Source” option allows
you to explore different compendia (the same ones as visible in
the various eFP Browser views described earlier), while the
“Tissues” option allows you to choose which tissue or condition within a given compendium you are interested in using to
retrieve expression level data for painting onto the nodes. In
this case, we will examine the expression levels in Seeds Stage
10 w/o Siliques in the Developmental_Map data source by
selecting these and toggling the Overlay Expression button.
These data are mostly from Schmid et al. [25]. In this case we
see that ABI3 and ABI5 (but not the other interactors) are both
strongly expressed in the seeds at later stages of development,
consistent with their known biological roles. It is possible to
explore the expression levels for the corresponding nodes
(genes) by selecting different data sets and tissues/conditions
to permit you to identify other tissues in which other nodes are
more strongly expressed (e.g., Tissue_specific / Guard Cells no
ABA).
3.11 Integrated Tools
Integrated tools associate data from multiple heterogeneous
sources of genomic data to obtain more accurate predictions.
Most of the bioinformatics tools described in this section integrate
protein and genetic interactions, pathways, coexpression,
co-localization and protein domain similarity and allow the user
generate hypotheses in a rapid and facile manner.
3.11.1 VirtualPlant
VirtualPlant [68] integrates genomic data from different sources
(see Note 24) and provides a set of tools to visualize and analyze
these data. One extremely useful attribute of VirtualPlant is that
data and analyses can be stored on the website.
1. Go to http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/. If
you wish to store your data, click on “Login” to register. The
dark blue navigation bar at the top of the page contains the
different VirtualPlant tools.
2. Click on “Query.” To perform a query, select an option on the
type list (i.e., genes) and add a keyword (e.g., ABI3). The
results are displayed in a table; click on the gene that best
matches your query (i.e., ABI3, At3g24650). VirtualPlant
shows all the information available on the server about our
query, including annotation, gene models, and external links.
For additional data click on the “Gene Family” folder to see
more members of the ABI3VP1 transcription factor family—
the ABI3VP1 family has 11 members.
Arabidopsis Bioinformatics
71