Open a Study and Start Exploring

This guide shows you how to open a study in Omics Studio and explains the features you will see in the Explorer view. After following these steps you will know how to navigate the main sections of the Explorer and understand what each section offers.

1. Open a study

1. From the Workspace menu, choose Projects & Studies. You will see a list of projects with their studies nested underneath.
2. Find the project containing your study and click the study row to highlight it.
3. At the top navigation bar, click Explorer. Omics Studio loads the selected study in the Explorer view (the breadcrumb at the top shows the current project and study).

Note: The left-hand arrow in each study row may not open the Explorer directly; using the Explorer link in the top menu ensures the highlighted study is opened.

Once the Explorer view opens, the left pane displays the EXPLORER menu. This menu provides access to several tools that help you examine and analyze your data.

2. Study Preferences

The Study Preferences section lets you define default parameters that will be used across analyses. Setting these preferences up front helps maintain a consistent focus and saves time later. Key panels include:

• Identifier preferences: Choose identifiers for expression (e.g., UniProt ID for proteomics) and metabolite data (e.g., ChEBI ID). These identifiers are used throughout analyses and in annotation databases.
• Expression preferences: Set a Valid Value threshold (e.g., 70%) to filter low-quality expression values and optionally pre-select specific samples.
• Statistical preferences: Define defaults for statistical thresholds. You can select one or more comparisons from available contrasts (such as Group A vs Group B) and set cut-offs for P-value, Adjusted P-value, and log2 fold-change thresholds (both up- and down-regulated).
• Database preferences: Select a default annotation database for enrichment analyses.
• Reset/Save buttons: After adjusting preferences, click Save Study Preferences to store your changes or Reset Study Preferences to revert to defaults.

These settings can be adjusted later during analysis wizards, but setting them early provides sensible defaults for the study.

3. Statistics View

The Statistics View section provides an interface for visualizing and comparing statistical results. A brief overview explains that this tool helps you identify potential biomarkers by comparing statistical metrics such as significance levels, fold changes and correlation patterns.

You can click Start your statistical analysis to launch an interactive workflow that displays volcano plots, correlation plots and other visualizations based on your selected comparisons and thresholds.

4. Enrichment Analysis

Expanding the Enrichment Analysis item reveals two types of enrichment workflows:

4.1 Over-Representation Analysis (ORA)

ORA identifies biological processes or pathways that are over-represented in a list of genes, proteins or metabolites. After you have run ORA, the results appear in a table and bar chart view. Notable features include:

• Results table: Shows each enriched term with columns for Group, ID, Description, Gene Ratio and Background Ratio. You can select rows using checkboxes and page through results.
• Plots: Switch between a bar chart and table. The bar chart gives a quick visual summary of the top enriched pathways.
• Focus pane: On the right side, you can filter results by comparisons (e.g., Group A vs Group B), limit the display to the top 15 pathways, set p-value or gene-ratio filters, and view related identifiers. Selecting rows adds them to the Current Selection list for downstream analysis.

4.2 Gene Set Enrichment Analysis (GSEA)

The Gene Set Enrichment Analysis section introduces GSEA and provides a button to start a new GSEA workflow. GSEA evaluates whether predefined gene sets show statistically significant expression differences between conditions and is helpful when you want to consider coordinated changes in entire pathways rather than individual genes.

5. Database Search

The Database Search section lets you query external annotation databases to explore details about genes, proteins or metabolites. Features include:

• Database categories: Tabs for UniProt Knowledgebase, Reactome, Human Protein Atlas and other resources. Each category is subdivided into modules such as Molecular Identity, Structure & Features, Function & Interaction, and Expression.
• Search and navigation: Use the search box to find specific identifiers. You can jump to a particular page of results via the page input. Results are shown in a table, and selecting a row displays detailed annotations in the right-hand Details pane.

Database search is useful for verifying protein identities, exploring pathway membership or retrieving structural information without leaving Omics Studio.

6. My Lists

The My Lists section allows you to manage custom lists of identifiers for reuse across analyses. You can:

• Create a new list: Click Create New List and provide a name.
• Add items: Use Add to list to include selected identifiers from statistics, enrichment or database search results.
• Export a list: Download a list of identifiers for use outside of Omics Studio.
• Select existing lists: The right panel shows all your lists; select one to view its contents in the table.
• Organise lists: Lists can be renamed or deleted using the context menu next to each list.

Summary

When you open a study and enter the Explorer, Omics Studio presents a structured environment for configuring defaults, performing statistical analyses, running enrichment analyses, searching annotation databases and managing identifier lists. Understanding these sections helps new users navigate the platform and make the most of their omics data.