Analysis Tools

AmpliconRepository.org provides powerful tools for searching, filtering, and analyzing focal amplification data across projects and samples.

The search functionality allows you to find specific genes, projects, or classifications across the entire repository. You can access the search via the Search button in the navigation bar.

Advanced Search Features

  • Wildcards: Use * to match partial names. For example, CCLE* will find all projects starting with CCLE, and MYC* will find all genes in the MYC family.
  • Logic Operators:
    • Use | for OR logic (e.g., MYC|EGFR finds amplifications containing either gene).
    • Use & for AND logic (e.g., MYC&EGFR finds amplifications containing both genes).
  • Metadata Search: Collapse the metadata section to search by:
    • Sample Type: (e.g., "cell line", "primary tumor")
    • Cancer Type or Tissue: (e.g., "Glioblastoma", "Lung")

Filtering Results

In the search results page, you can further refine the list of samples using the Project Filters sidebar. This allows you to toggle specific projects on or off to focus your analysis on specific cohorts.

Co-amplification Graph Analysis

The Co-amplification Graph tool (available in the navigation bar) allows you to visualize significant gene-gene associations across multiple projects.

How to use the tool:

  1. Select Projects: Select one or more projects from the list.
    • Note: All selected projects must use the same reference genome group (hg19/GRCh37 OR hg38/GRCh38).
  2. Generate Graph: Click "Generate Coamplification Graph."
  3. Adjust Thresholds: Use the sliders to filter the graph:
    • Significance Threshold: Filter edges based on the chi-squared significance score (q-value).
    • Co-amplification Frequency: Filter edges based on how often the genes appear together in the same amplicons.
  4. Visualize: Interact with the graph to see how genes cluster together.

Data Export

You can download the graph data as a CSV file containing the edges and their associated scores for further offline analysis.

Batch Downloads

You can download large numbers of samples at once directly from the search results page.

  1. Perform a search to find your samples of interest.
  2. Use the Select All or individual checkboxes to select samples.
  3. Click Download Selected Samples.

Large Downloads: For batches larger than 100 samples, the system will process your request in the background. Once the zip archive is ready, you will receive an email with a secure download link (S3 presigned URL).