Biology Reference
In-Depth Information
Fig.
1
A representative omics aspect in the Soybean Proteome Database [
15
]. (
a
) Proteome, transcriptome,
and metabolome data are associated by an omics table. Proteomic data include 2-DE images and temporal
expression profi les in the seedling stage in soybean. Transcriptomic and metabolomic data also include
temporal profi les of the entities. Metabolites are mapped on metabolic pathways, as are associated mRNAs
and proteins. (
b
) An example omics table in the database. The table indicates signifi cant relationships between
mRNAs, proteins, and metabolites with cells of the same color
Protein sequences and structures are linked to information about
the genes such as gene models. Furthermore, metabolomics data
from the SoyMetDB database [
53
] are incorporated into SoyKB.
2.4 Web-Based
Proteomic Tools and
Prediction Programs
The Web site provides a tool for spot visualization on gel images
[
21
]. Users can upload gel images and coordinates/information
spreadsheets. The Web site also gives access to functional annotation
of identifi ed proteins defi ned by the user, and annotation of several
proteins per analyzed protein “spot” according to MS data.
Previously, this type of gel image-based database had to be opened
through a server computer that users set up by themselves using a
software tool such as the Make 2D-DB II package [
52
]. With
GelMap a user can open the gel-based image data through the
GelMap Web site without having to use a server.
2.4.1 GelMap
This Web site provides a tool for prediction of subcellular localiza-
tion of plant proteins with single or multiple sites. A new prediction
2.4.2 iLoc-Plant
