Database Usage

The user interface of the DroughtDB consists of four main navigation areas: the main menu (A) at the top right, the Gene Table (B), the Pathway Browser (C), and the Reset and Export Buttons on the lower left.

A. Main Menu

The main menu is used to navigate between the different pages of the DroughtDB. Besides this help page and the database, we provide a link to an update form. Every support from the research community enrich the DroughtDB with updates and newly published papers and findings is welcome. To facilitate this we provide a user submission system. You can click onto the DroughtDB logo on the top left to return to the start page. The content of the form is based on the export entries 'D'.


B. Gene Table

The Gene Table initially provides an alphabetical list of all drought-related genes and gene identifiers available in the DroughtDB. When hovering with the mouse cursor over a table row (i.e. gene entry) from the Gene Table, all corresponding nodes in the Pathway Browser are highlighted. Clicking onto a table entry with the left mouse button opens a tool-tip window with further details to the selected gene:

Entry Brief Description
Gene Gene name.
ID Official gene identifier that is used/referenced in public databases.
Organism The organism referenced in the publication, i.e. that was used to describe the gene functionality.
Function Short information about the functionality of the gene.
Phenotype The phenotype of the gene.
Reference & PMID The publication where the respective gene was found. A link to the PMID entry is provided, if available.
OrthoMCL Groups A list of OrthoMCL orthologous groups is provided, if available/computable. The list is ordered by organism name(s). Also references to the PGSB PlantsDB and other external sources are given, if available.
Sequence The sequence information for the respective gene is provided.

In the OrthoMCL analysis, following protein sequence datasets were used to identify orthologous groups:

Dataset Source
Aegilops tauschii BGI annotation
Arabidopsis thaliana TAIR10 annotation
Brachypodium distachyon MIPS v1.2
Hordeum vulgare IBSC annotation HC genes
Oryza sativa MSU7 annotation
Secale cereale MSU7 annotation
Solanum lycopersicum ITAG v2.3
Sorghum bicolor MIPS v1.4
Zea mays Annotation release 5b

C. Pathway Browser

The Pathway Browser is providing a simplified interactive interface to the pathways for molecular and physiological adaptation. Clicking onto a node reduces the list of genes in the Gene Table to the ones that are related to the selected node. A small flag marks the selected node. Hovering above a node in the tree highlights corresponding genes in the Gene Table and a tool-tip appears showing the number of associated genes. If a selection was made, the number nodes relative to the selection are shown as well.


D. Reset/Export Function

Tow buttons in the lower left section are of relevance if a subset of genes was selected. They either allow to deselect all genes and put the DroughtDB back to its initial state; or the selected genes can be exported.

In case of an export the selected genes shown in the Gene Table will be exported into a Comma Separated Value (CSV) formatted file: columns are separated by commas, entries additionally indicated by apostrophes. The Tags can be used to categorize the gene by its pathway(s). The following data structure will be exported:

Column Header Example Entry
Gene RGS1
ID AT3G26090
Organism Arabidopsis thaliana
Biological Function regulator of G-protein signaling
Phenotype overexpression: increased drought tolerance
Reference Chen et al., 2006
Tags Growth Control;Root/Leaf Development;Regulatory Proteins;Signal Transduction;Others

Reference

Svenja Alter, Kai C. Bader, Manuel Spannagl, Yu Wang, Eva Bauer, Chris-Carolin Schön, Klaus F.X. Mayer (2014)
DroughtDB: An expert-curated compilation of plant drought stress genes and their homologs in nine species.

Background image by Florence Devouard; licensed under CC-BY-SA.3.0; via Wikimedia Commons.