Search and filter by experimental conditions. AraLightDEGs includes a total of 58 experimental conditions, with four outliers excluded from the search by default (active checkbox "Remove outlier stress conditions from analysis").
You can use two default
quick search settings to retrieve the data:
• To search for the short response DEGs (0–90 minutes), click the "Quick search for short response DEGs" button;
• To search for the medium and long response DEGs (120 minutes–3 days), click the "Quick search for medium and long response DEGs" button.
To perform a
specific search for DEGs, you can apply the following filters:
• Light intensity: Set the desired range ("Minimum/Maximum light intensity");
• Tissue type: Select "Leaves", "Seedlings", or both;
• Age of plants: Set the desired range ("Minimum/Maximum plant age");
• Exposure time: Define the duration of high light treatment ("Minimum/Maximum duration of high light treatment").
After selecting the relevant filters, click "Search in AraLightDEGs" to retrieve the results.
Filters by gene identifiers, Gene Ontology, and transcription factors.
To search for a specific set of genes and analyze their transcriptional response to high light, use the "Search for specific
Arabidopsis thaliana genes" filter. To find DEGs associated with specific
Gene Ontology (GO) terms, use the input option "Search for specific Gene Ontology (GO) terms". If you are specifically interested in transcription factors, enable the "Limit results to transcription factors only" checkbox.
Additionally, DEGs can be filtered based on:
• Frequency of identification: Use the "Minimum frequency threshold" option. Frequently identified DEGs represent universal high light response genes, while rare DEGs are condition-specific.
• Expression threshold: Set a "Minimum average expression" in counts per million (CPM) to refine the selection.
Sorting the results. The "Sort results by" option (8 values) defines the sorting order of the output results, in descending order.
DEGs can be sorted by:
• Frequency of occurrence: as (1) upregulated, (2) downregulated, or (3) total frequency (upregulated and downregulated);
• Average fold change: for (4) upregulation or (5) downregulation;
•
Transcription factor family name (6);
• Average high light intensity at which they were detected (7);
• Average treatment duration at which they were detected (8).
Selecting the DEGs of interests and exporting to STRING.
After performing a search, the resource generates two histograms displaying the frequency of upregulated and downregulated DEGs based on the selected search conditions and filters. From these histograms, you can select genes of interest (for example, the most frequently upregulated ones) using the options "Select DEGs regulation type", "Select the DEGs with minimal/maximal frequency". The selected genes can be downloaded as a simple list using the ("Download the gene identifiers of selected DEGs") button or submitted as a query for protein-protein interaction network reconstruction in
STRING using the ("Reconstruct the protein-protein interaction network") button.
The main results are displayed in a table at the bottom of the webpage, with 1,000 rows per subpage. The full output table can be downloaded using the "Download the results" button. Additionally, you can customize the downloaded data by selecting optional information in the "Include in the downloadable results table" section. The available options (seven checkboxes) include:
•
Gene description;
• Transcription factor family;
• Gene Ontology terms;
• Full lists of experimental conditions and their corresponding differential expression values.