Analysis of public microarray data sets

Trainer St├®phane Plaisance
BITS Courses TRAINING AT VIB

Goal

This training only handles the analysis of publicly available microarray data sets. To learn how you can analyze your own data, we refer to the "Analysis of Affymetrix microarrays using free Affymetrix software" training.

Summary

This training will give you an overview of what GEO has to offer. Several experiments will be analyzed using simple tools to obtain differential gene lists. An introduction to downstream tools dedicated to functional enrichment will close the session.

Prerequisites

This training is meant for biologists with little or no data of their own that need to identify genes of interest associated to a given biological problem.? The participants do not need any prior knowledge of programming. If you have no experience with microarrays, you can follow the introduction to Affymetrix microarray analysis training or consult the training material of this introduction.

Schedule

Morning session

  • Search GEO to find public datasets related to one's project
  • Compute differential expression using public tools to identify specific biomarkers associated with distinct conditions or sample groups:
    • RobiNA as a standalone desktop tool
    • GEO2R within the NCBI web-portal and after transfer to RStudio
    • Genevestigator will not be used during this session and is detailed during a separate training
  • Perform functional enrichment on the obtained lists to identify key biological functions over-represented in the data using public tools:

Afternoon session

  • The CLC Main workbench (only available for VIB users)
  • Users perform their own queries with assistance from the trainer

Training material

There is no training material available for this course.

Links

None

Scientific topics Microarray data rendering, differential expression analysis, GEO accession number
Target audience Life Science Researchers, PhD students, post-docs