Analyze public microarray data using Genevestigator

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[ Main_Page | Genevestigator_training ]

Date: October 23rd, 2015 from 13h00 to 17h00

Goal

  • Understand what Genevestigator[1] is
  • Learn how to use Genevestigator to characterize your genes of interest
  • Identify and prioritize novel targets or biomarkers
  • Interpret lists of genes by grouping them by their response to biological contexts
  • Learn how to combine Genevestigator with other software to answer biological questions

Handicon.png This half-day training will not be sufficient to become fluent in the GV 'language'. Please consider spending quality time in Genvestigator and build your own circular pipelines to discover and document biomarkers based on the different experimental facets available for filtering

Summary

This training will give you an overview of the possibilities of Genevestigator, a search engine of curated and normalized publicly available gene expression data. The interface allows you to visualize spatio-temporal (tissue - developmental stage) and perturbational gene expression information of many species in a user-friendly graphical way.

The hands-on part of this training includes concrete examples of downstream software that can be used to further interpret the results of your Genevestigator searches, like Ingenuity Pathway Analysis, DAVID, or more recent alternatives. Finally, you will be able to start exploring with questions from your own research under the supervision of the trainer.

Technical.png You may be limited by the allowed concurrent VIB access to IPA when using your own account after this session


gv_workflow.png

Exercises

You will find in this section exercises used during the hand-on session. Solutions are collapsed to stimulate your curiosity, try to play fair!.

click here to go to the Genevestigator login page

  • GV Exercise.1 Identify control probes/genes to be used in QPCR for your probes/genes of interest.
  • GV Exercise.2 Identify probes/genes specific for a given experimental context.
  • GV Exercise.3 Explore the GV interface with workspace data created above
  • GV Exercise.4 Discover context specificity for a list of probes
  • GV Exercise.5 Identify tumor markers and perform downstream functional analysis
  • GV Exercise.6 Find similarity between samples and/or conditions
  • GV Exercise.7 Create and/or use expression signatures
  • GV Exercise.8 Find other probes that are co-expressed with a given probe [one probe at a time]

Today's main tools

  • Commercial tools (VIB license)
  • Public tools to create gene lists
  • Public tools to analyze gene lists
  • Next generation enrichment tools
  • For Plant scientists
  • Older but still valid tools
  • Still need more tools!

Links and online tutorials

More Info

  • On the VIB website: [4]
  • On the BITS website: [5]

References:
  1. Philip Zimmermann, Matthias Hirsch-Hoffmann, Lars Hennig, Wilhelm Gruissem
    GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.
    Plant Physiol.: 2004, 136(1);2621-32
    [PubMed:15375207] ##WORLDCAT## [DOI] (P p)

  2. Sebastian Proost, Michiel Van Bel, Dries Vaneechoutte, Yves Van de Peer, Dirk Inzé, Bernd Mueller-Roeber, Klaas Vandepoele
    PLAZA 3.0: an access point for plant comparative genomics.
    Nucleic Acids Res.: 2015, 43(Database issue);D974-81
    [PubMed:25324309] ##WORLDCAT## [DOI] (I p)

  3. http://omictools.com

    Vincent J Henry, Anita E Bandrowski, Anne-Sophie Pepin, Bruno J Gonzalez, Arnaud Desfeux
    OMICtools: an informative directory for multi-omic data analysis.
    Database (Oxford): 2014, 2014;
    [PubMed:25024350] ##WORLDCAT## [DOI] (I e)

  4. http://www.vib.be/en/training/research-training/courses/Pages/Analysis-of-public-microarray-data-using-Genevestigator.aspx
  5. https://www.bits.vib.be/index.php/training/125-genevestigator



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