can adjust and select different types of normalization and
whether we prefer count value by clicking the small boxes on
the right side.
4. We can then select a specific sample by clicking on top of the
box containing its count values. Once selected, TraVA automatically changes the values shown to fold changes in regard to
the selected sample. This allows us to easily visualize which
samples are significantly different to our reference sample. By
default, the statistically significant differences are calculated
using DESeq. However, we can choose other algorithms such
as DESeq2 or BaySeq by selecting them using the boxes on the
right side.
3.4.4 Genevestigator
Data from 10,000+ high-quality ATH1 arrays are available for
Arabidopsis from Genevestigator (https://www.genevestigator.
com/gv/) [29]. As with the eFP Browser, the different tools of
this resource let us determine when and where our gene of interest
is expressed and in response to which conditions. The main difference between the eFP Browser and Genevestigator is that data are
displayed in heatmap format as opposed to a pictograph. One of the
major advantages of this tool is the simultaneous analysis of
hundreds or thousands of genes in a biological context, as opposed
to the eFP Browser, which permits a user to examine only one gene
at a time (see Note 8).
1. Go to https://www.genevestigator.com/gv/ and select “Plant
Biology” under “Application areas.” Click on “INSTALL
APP” on the subsequent page. Follow the instructions to get
Genevestigator running on your computer—will need to have
the correct Java version, and also a username/password (plus,
request free access to Genevestigator Professional at the bottom
of your user account page).
2. Click “New” in the Data Selection panel on the left, then
choose “Arabidopsis thaliana” as the Organism, “Affymetrix
Arabidopsis ATH1 Genome Array” as array type, and don’t
select any Filters (see Note 9). Click OK.
3. Introduce the AGI ID by clicking on “New” in Gene Selection
panel of the main window. In our case, we enter the ABI3 AGI
ID, “At3g24650.” Click OK.
4. The Condition Search tools gives us gene expression data from
the different array sets (see Note 10), the filled dots indicate
detection p-values under 0.06 and the unfilled p-values over
0.06 (see Note 11). On the “Samples” tab we can examine the
expression in all the available arrays. To get the experimental
design and gene expression information, just move the mouse
over the sample name or the dot.
40
G. Alex Mason et al.
whether we prefer count value by clicking the small boxes on
the right side.
4. We can then select a specific sample by clicking on top of the
box containing its count values. Once selected, TraVA automatically changes the values shown to fold changes in regard to
the selected sample. This allows us to easily visualize which
samples are significantly different to our reference sample. By
default, the statistically significant differences are calculated
using DESeq. However, we can choose other algorithms such
as DESeq2 or BaySeq by selecting them using the boxes on the
right side.
3.4.4 Genevestigator
Data from 10,000+ high-quality ATH1 arrays are available for
Arabidopsis from Genevestigator (https://www.genevestigator.
com/gv/) [29]. As with the eFP Browser, the different tools of
this resource let us determine when and where our gene of interest
is expressed and in response to which conditions. The main difference between the eFP Browser and Genevestigator is that data are
displayed in heatmap format as opposed to a pictograph. One of the
major advantages of this tool is the simultaneous analysis of
hundreds or thousands of genes in a biological context, as opposed
to the eFP Browser, which permits a user to examine only one gene
at a time (see Note 8).
1. Go to https://www.genevestigator.com/gv/ and select “Plant
Biology” under “Application areas.” Click on “INSTALL
APP” on the subsequent page. Follow the instructions to get
Genevestigator running on your computer—will need to have
the correct Java version, and also a username/password (plus,
request free access to Genevestigator Professional at the bottom
of your user account page).
2. Click “New” in the Data Selection panel on the left, then
choose “Arabidopsis thaliana” as the Organism, “Affymetrix
Arabidopsis ATH1 Genome Array” as array type, and don’t
select any Filters (see Note 9). Click OK.
3. Introduce the AGI ID by clicking on “New” in Gene Selection
panel of the main window. In our case, we enter the ABI3 AGI
ID, “At3g24650.” Click OK.
4. The Condition Search tools gives us gene expression data from
the different array sets (see Note 10), the filled dots indicate
detection p-values under 0.06 and the unfilled p-values over
0.06 (see Note 11). On the “Samples” tab we can examine the
expression in all the available arrays. To get the experimental
design and gene expression information, just move the mouse
over the sample name or the dot.
40
G. Alex Mason et al.