News & Updates

AMP PD has launched its first Community Workspace on the AMP PD Knowledge Platform

Introducing the AMP PD RNA-Seq Explorer

As part of an ongoing effort to share community developed workspaces with the research community, AMP PD has launched its first community workspace featuring the USC Gene Explorer. The Gene Explorer is a visualization tool for individual and summary level data within the Terra-based AMP PD Knowledge Platform, developed and hosted by the Dr. David Craig Laboratory at the University of Southern California (USC). It features a set of dynamic and interactive tools for exploring clinical and molecular transcriptomics data.

The Gene Explorer is accessible for Tier 2 AMP PD users in Terra.

Need access to the Gene Explorer?

  • New users can register with AMP PD here
  • Registered Tier-1 users can request access to Tier-2 resources by contacting the AMP PD Access and Compliance Team (ACT) via email, act@amp-pd.org

The AMP PD RNA Explorer has four primary functions:

  1. Data & Methods Links. Used for accessing methods, downloading meta-data tables, and finding location primary data and notebooks in the AMP PD Terra workspace.
  2. Visualization of Quality Metrics. Visualization and exporting of quality metrics, such as principal component analysis, reads generated, batch effects, and other quality parameters.
  3. Cohort Level Differential Expression Analysis. Visual exploration of pre-calculated cohort level analysis for differential expression, including volcano-plots.
  4. Gene/Position Level Browsing. Exploration and downloading of individual/summary level data either by searching for a gene or by genomic position.

 

Gene Browsing

The Gene Explorer workspace includes instructions and an example showing how to explore genes. In the example, the gene SNCA shows both a gene-level view and a genomic position view of data from AMP PD. Plots allow for dynamic graphics over various parameters such as visit or disease status. Underlying data can be exported to other tools like Excel.

This application is developed by the USC Institute of Translational Genomics and you can learn more about our research informatic tools through at https://itg.usc.edu.

Please send any questions and requests related to the RNA-seq Data Explorer App to davidwcr@usc.edu.