OMICs viewer and Show Data “As a table of pathway diagrams” and select the number of pathways to show, such as
25 (the OMICS Viewer uses a “Pathway Perturbation Score”
to rank the pathways according to their overall increase or
decrease in expression. The pathways are shown in a table.
5. LEC1OX appears to promote gibberellin biosynthesis through
the activation of genes involved in that metabolic pathway, such
as GA20 oxidases 3 and 7. LEC1 acts as a positive regulator
upstream of ABI3 [56], as ABI3 is upregulated in LEC1 plants.
As we have seen in data sets contained in Genevestigator, the
GA biosynthetic inhibitor paclobutrazol inhibits ABI3 expression. It appears that LEC1 and ABI3 could play a role in the
crosstalk between ABA and GA pathways, which supports the
known influence of these genes in these pathways.
3.8.2 Pathway
Visualization: MapMan
One of the most widely used software for pathway visualization is
MapMan [51]. This software classifies genes and metabolites in
ontologies based on metabolic pathway, cellular function,
biological response, and gene families. The main advantage is that
the user can download the software and work offline. Also, the
databases associated with MapMan are well annotated and are easily
downloadable in a format that is useful for bioinformaticians.
1. Go to http://mapman.gabipd.org/web/guest/mapmandownload and download the latest version of MapMan (see
Note 23). Open MapMan.
2. Once open, the software shows the “get started” window that
will help us on the tool use. Basically, MapMan works by
combining a data file (experimental results) with diagrams
(pathways or chromosomal views) and mapping information.
Every file is stored in a specific folder (left side of the program).
Before starting the analysis, it is worth exploring the files
available in MapMan (pathways and mapping files). To download more pathways or mapping files from the MapManStore
server, click “File,” “Add pathway,” or “Add mapping,” click
“Download” and choose a pathway/map from the list, i.e.,
download the last gene TAIR annotation.
3. Upload your data by clicking on the folder icon at the top left
of the screen. Data must be in .xls or a tab delimited .txt file, the
first column should contain the AGI ID (or Affymetrix ID)
numbers and the second column, the expression values. The
data will be stored in the “Experiments” folder. We will use the
genes upregulated in the LEC1OX plants present in Mu et al.
[10]. Download the file here if you didn’t already for the
AraCyc OMICS viewer section (see Note 1).
4. For visualization of the data, choose a pathway from the left
and double click, i.e., “Regulation overview.” Choose a
Arabidopsis Bioinformatics
63
25 (the OMICS Viewer uses a “Pathway Perturbation Score”
to rank the pathways according to their overall increase or
decrease in expression. The pathways are shown in a table.
5. LEC1OX appears to promote gibberellin biosynthesis through
the activation of genes involved in that metabolic pathway, such
as GA20 oxidases 3 and 7. LEC1 acts as a positive regulator
upstream of ABI3 [56], as ABI3 is upregulated in LEC1 plants.
As we have seen in data sets contained in Genevestigator, the
GA biosynthetic inhibitor paclobutrazol inhibits ABI3 expression. It appears that LEC1 and ABI3 could play a role in the
crosstalk between ABA and GA pathways, which supports the
known influence of these genes in these pathways.
3.8.2 Pathway
Visualization: MapMan
One of the most widely used software for pathway visualization is
MapMan [51]. This software classifies genes and metabolites in
ontologies based on metabolic pathway, cellular function,
biological response, and gene families. The main advantage is that
the user can download the software and work offline. Also, the
databases associated with MapMan are well annotated and are easily
downloadable in a format that is useful for bioinformaticians.
1. Go to http://mapman.gabipd.org/web/guest/mapmandownload and download the latest version of MapMan (see
Note 23). Open MapMan.
2. Once open, the software shows the “get started” window that
will help us on the tool use. Basically, MapMan works by
combining a data file (experimental results) with diagrams
(pathways or chromosomal views) and mapping information.
Every file is stored in a specific folder (left side of the program).
Before starting the analysis, it is worth exploring the files
available in MapMan (pathways and mapping files). To download more pathways or mapping files from the MapManStore
server, click “File,” “Add pathway,” or “Add mapping,” click
“Download” and choose a pathway/map from the list, i.e.,
download the last gene TAIR annotation.
3. Upload your data by clicking on the folder icon at the top left
of the screen. Data must be in .xls or a tab delimited .txt file, the
first column should contain the AGI ID (or Affymetrix ID)
numbers and the second column, the expression values. The
data will be stored in the “Experiments” folder. We will use the
genes upregulated in the LEC1OX plants present in Mu et al.
[10]. Download the file here if you didn’t already for the
AraCyc OMICS viewer section (see Note 1).
4. For visualization of the data, choose a pathway from the left
and double click, i.e., “Regulation overview.” Choose a
Arabidopsis Bioinformatics
63