Omics Studio | Documentation

Appearance

Statistics View ​

Overview ​

The Statistics View in Omics Studio provides an interactive environment for exploring statistical results derived from expression data, such as differential expression analyses. It enables users to filter, visualize, and compare features based on statistical metrics like p-values, adjusted p-values, and log2 fold changes, helping to identify biologically meaningful signals and potential biomarkers.

The Statistics View is designed for rapid exploration and prioritization of results before downstream analyses such as pathway enrichment or network visualization.

Accessing the Statistics View ​

  1. Open a study in the Explorer
  2. In the left-hand navigation, select Statistics View
  3. Click Start your statistical analysis

Step 1 – Define Analysis Criteria ​

Select Your Comparisons ​

  • Choose one or more statistical comparisons (e.g. ConditionX vs ConditionY)
  • Comparisons are derived from statistics files associated with the study
  • Multiple comparisons can be selected simultaneously

After selecting comparisons, click Continue.

Step 2 – Choose Your Plots ​

While the data is being processed, select which visualizations to generate:

  • Dot Plot
  • Volcano Plot

You can always add or remove plots later.

Click Continue once processing is complete.

Results Interface Overview ​

The Statistics View consists of three main areas:

  • Results Panel (center) – tables and plots
  • Explorer Navigation (left) – switching between views
  • Focus Panel (right) – filters, comparisons, and selections

Table View ​

Description ​

The Table view displays statistical results in a tabular format, with one row per feature (e.g. gene or protein).

Typical columns include:

  • Comparison
  • Identifier
  • Log2 Fold Change
  • Fold Change
  • p-value
  • Adjusted p-value

Table Features ​

  • Search across all columns
  • Sort by any column
  • Pagination with adjustable rows per page
  • Download table as a file
  • Select individual or multiple rows using checkboxes

Selected features appear in the Current Selection section of the Focus panel.

Focus Panel ​

The Focus panel allows dynamic filtering and refinement of the results without rerunning the analysis.

Comparisons ​

  • Displays the currently active comparisons
  • Comparisons can be added or removed at any time

Filters ​

Available filters include:

  • Top 15 (lowest p-value)
    Displays only the top-ranked features based on p-value

  • p-value
    Filters features based on raw p-value threshold

  • Adjusted p-value
    Filters features based on multiple-testing corrected p-values

  • Upregulation (Log2 Fold Change)
    Shows features with positive log2 fold change

  • Downregulation (Log2 Fold Change)
    Shows features with negative log2 fold change

  • Select from My Lists
    Restricts results to features contained in a predefined list

Filters can be combined to narrow down results efficiently.

Current Selection ​

  • Displays features selected from the table or plots
  • Selected features can be added to My Lists or used in downstream analyses

Dot Plot View ​

Description ​

The Dot Plot visualizes statistical results across comparisons.

  • Each dot represents a feature
  • Dot color encodes log2 fold change
  • Dot size represents –log10(p-value)
  • The x-axis represents the comparison
  • The y-axis lists feature identifiers

Features ​

  • Zoom and pan
  • Hover tooltips for detailed values
  • Download plot as an image
  • Automatic limiting to top 100 features (by p-value) for performance

A warning is displayed when too many points would be shown, prompting users to apply filters.

Volcano Plot View ​

Description ​

The Volcano Plot displays statistical significance versus magnitude of change.

  • X-axis: Log2 Fold Change
  • Y-axis: –log10(p-value)
  • Each point represents a feature

Interpretation ​

  • Features far left or right show strong down- or upregulation
  • Features high on the y-axis are more statistically significant
  • Threshold lines may indicate significance cutoffs

Features ​

  • Zoom and pan
  • Box or lasso selection
  • Hover to inspect feature details
  • Download plot as image

Best Practices ​

  • Apply p-value or adjusted p-value filters early to reduce noise
  • Use log2 fold change filters to focus on biologically meaningful changes
  • Combine Table and Plot views for complementary perspectives
  • Add selected features to My Lists for reuse in enrichment or pathway analyses

Summary ​

The Statistics View is a central tool in Omics Studio for exploring and prioritizing statistically significant features. Through interactive tables, dot plots, and volcano plots—combined with flexible filtering—the Statistics View supports efficient identification of candidates for further biological interpretation and downstream analysis.