3.9 Protein
Information
3.9.1 Protein
Information: SUBA4
The subcellular location database for Arabidopsis proteins is a comprehensive resource encompassing experimental (“direct assay”)
data from more than 1,768 publications, in which 11,740 proteins
have annotated subcellular localizations based on chimeric fusion
studies or subcellular proteomic studies [57]. In addition, subcellular localization predictions generated by 22 algorithms are also
provided. It is possible to specify which you would like to retrieve
from the SUBA database on the input page. Alternatively, one can
query in a general manner, either for a single gene or for a list of
genes, as follows:
1. Go to http://suba.live/. Click on the “Search” tab, then the
“Protein name & properties” tab and scroll down to the section that is labeled “alias, family IDs or protein sequence.”
Type in “ABI3.” Click on the green “+” icon to add it to the
search criteria, then scroll up and click on the button labeled
“Query.”
2. You will be taken to a new tab with the query results.
3. Click on “AT3G24650.1” under AGI. You will be redirected
to a database factsheet page.
4. We know ABI3 is a transcription factor, but if we look at the
Predictors window, users can also see that ABI3 could be
located in the mitochondria and endoplasmic reticulum,
among other cellular compartments.
5. Go back to the first page (http://suba.live) and click the
“Clear” button beside the “Query” button. Assume we know
that we want to investigate a mysterious transcription factor
related to FUS3 and LEC1. Under “protein description” (not
where you entered the gene name before), type in FUS3, then
click on the green “+” button. Delete the contents of the text
box and replace it with “LEC1” and “transcription factor,”
clicking on the green “+” button in between.
6. Click on the query button. This should return ABI3.
3.9.2 Protein
Information: Cell eFP
Browser
There is an alternative, easier way to obtain general information on
subcellular localizations. The Cell eFP Browser (one of the many
plant bioinformatic tools available at the Bio-Analytic Resource for
Plant Biology) is a simple tool that generates a graphical view of the
predicted and experimentally determined localizations generated/
curated by SUBA [24]. Cell eFP uses a simple heuristic algorithm
that weighs “direct assay” subcellular localization data higher than
prediction programs to provide a visual representation of where the
protein is localized within the cell. It provides a similar view to the
Cell eFP view in ePlant (Subheading 3.6.3). The color scale is not
dynamically adjusted, however.
Arabidopsis Bioinformatics
65
Information
3.9.1 Protein
Information: SUBA4
The subcellular location database for Arabidopsis proteins is a comprehensive resource encompassing experimental (“direct assay”)
data from more than 1,768 publications, in which 11,740 proteins
have annotated subcellular localizations based on chimeric fusion
studies or subcellular proteomic studies [57]. In addition, subcellular localization predictions generated by 22 algorithms are also
provided. It is possible to specify which you would like to retrieve
from the SUBA database on the input page. Alternatively, one can
query in a general manner, either for a single gene or for a list of
genes, as follows:
1. Go to http://suba.live/. Click on the “Search” tab, then the
“Protein name & properties” tab and scroll down to the section that is labeled “alias, family IDs or protein sequence.”
Type in “ABI3.” Click on the green “+” icon to add it to the
search criteria, then scroll up and click on the button labeled
“Query.”
2. You will be taken to a new tab with the query results.
3. Click on “AT3G24650.1” under AGI. You will be redirected
to a database factsheet page.
4. We know ABI3 is a transcription factor, but if we look at the
Predictors window, users can also see that ABI3 could be
located in the mitochondria and endoplasmic reticulum,
among other cellular compartments.
5. Go back to the first page (http://suba.live) and click the
“Clear” button beside the “Query” button. Assume we know
that we want to investigate a mysterious transcription factor
related to FUS3 and LEC1. Under “protein description” (not
where you entered the gene name before), type in FUS3, then
click on the green “+” button. Delete the contents of the text
box and replace it with “LEC1” and “transcription factor,”
clicking on the green “+” button in between.
6. Click on the query button. This should return ABI3.
3.9.2 Protein
Information: Cell eFP
Browser
There is an alternative, easier way to obtain general information on
subcellular localizations. The Cell eFP Browser (one of the many
plant bioinformatic tools available at the Bio-Analytic Resource for
Plant Biology) is a simple tool that generates a graphical view of the
predicted and experimentally determined localizations generated/
curated by SUBA [24]. Cell eFP uses a simple heuristic algorithm
that weighs “direct assay” subcellular localization data higher than
prediction programs to provide a visual representation of where the
protein is localized within the cell. It provides a similar view to the
Cell eFP view in ePlant (Subheading 3.6.3). The color scale is not
dynamically adjusted, however.
Arabidopsis Bioinformatics
65