User Guide: Differential Expression Analysis Visualization Tool

Welcome to our advanced differential expression analysis visualization platform. This user-friendly web application is meticulously designed to provide a comprehensive view of your differential expression analysis data through a range of visual representations.

1. Volcano Plot: Offers a visual perspective of log2 fold change against p-value/FDR, enabling the identification of significant gene changes.
2. MA Plot: Displays the relationship between average intensity and fold change, facilitating insights into data variance.
3. Bar Plot: Illustrates the intensity values across all conditions, providing an aggregate view.
4. Results Table: An interactive table to conveniently browse and review the results.

Currently, our platform supports visualization for experiments comparing two conditions.

Accepted File Type: Comma Separated Values (.csv)

Mandatory Columns:

• Gene_acc: A unique integer identifier for each gene. (Note: This won't be displayed in the results table.)
• Gene_id: Alphanumeric string indicating the gene or protein ID or their respective group for visualization.
• logFC: A decimal value indicating the log2 fold change between the two conditions being compared.
• log_AveExpr: A decimal value representing the log10 average intensity of the conditions.
• FDR: Decimal value detailing the false discovery rate.
• Desc: Descriptive text for the gene or protein groups.

Following the 'Desc' column, the intensity values for the two conditions should be presented.

Intensity Column Structure:

The intensity column header should adopt the format: {condition}_{replica}.

• {condition}: A concise label for the conditions being compared.
• {replica}: An integer indicating the replicate number.

Users can include any number of replicates. It's imperative that the {condition} label remains consistent across replicates. For instance: A_1, A_2, A_3, B_1, B_2, B_3 are appropriate headers for two conditions (A and B) with three replicates each (1, 2, 3). The platform extracts the condition names for display in the bar plot.

Ensure your file adheres to the format specified above for optimal results. We strive to offer a seamless and informative experience. Should you have further inquiries, please reach out to our support team.

Thank you for choosing our Differential Expression Analysis Visualization Tool. We wish you insightful discoveries!