Analyze public microarray data using Genevestigator
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Date: October 23rd, 2015 from 13h00 to 17h00
Contents
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
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.
You may be limited by the allowed concurrent VIB access to IPA when using your own account after this session
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)
- genevestigator: [https://genevestigator.com/gv/start/start.jsp]
- Ingenuity (IPA): [https://apps.ingenuity.com/ingsso/login?]
- genevestigator: [https://genevestigator.com/gv/start/start.jsp]
- Public tools to create gene lists
- BIOMART: [http://www.biomart.org/biomart/martview]
- QuickGO: [http://www.ebi.ac.uk/ego/]
- TAIR: [http://www.arabidopsis.org/tools/bulk/index.jsp]
- BAR: [http://bar.utoronto.ca/welcome.htm]
- BioCyc: [http://biocyc.org/gene-search.shtml]
- BioCyc Ath -> pathways: [http://biocyc.org/ARA/class-tree?object=Pathways]
- BioCyc Ath -> pathways: [http://biocyc.org/ARA/class-tree?object=Pathways]
- BIOMART: [http://www.biomart.org/biomart/martview]
- Public tools to analyze gene lists
- DAVID: http://david.abcc.ncifcrf.gov/summary.jsp is the father of enrichment tools and still does the job
- DAVID: http://david.abcc.ncifcrf.gov/summary.jsp is the father of enrichment tools and still does the job
- Next generation enrichment tools
- Enrich: http://amp.pharm.mssm.edu/Enrichr and its associated tool Lists2Networks use a respectable number of sources to compute enrichment
- WebGestalt: http://bioinfo.vanderbilt.edu/webgestalt is designed for functional genomic, proteomic and large-scale genetic studies
- encodeqt: http://encodeqt.simple-encode.org is using encode data to predict enriched TFs starting from a gene list
- Enrich: http://amp.pharm.mssm.edu/Enrichr and its associated tool Lists2Networks use a respectable number of sources to compute enrichment
- For Plant scientists
- PLAZA: http://bioinformatics.psb.ugent.be/plaza/ was developed at VIB and allows enrichment analysis of genes and gene lists (PLAZA-3 paper in NAR 2014 [2])
- PlantGSEA: http://structuralbiology.cau.edu.cn/PlantGSEA/
- PLAZA: http://bioinformatics.psb.ugent.be/plaza/ was developed at VIB and allows enrichment analysis of genes and gene lists (PLAZA-3 paper in NAR 2014 [2])
- Older but still valid tools
- ToppGene: http://toppgene.cchmc.org/prioritization.jsp]
- gProfiler: http://biit.cs.ut.ee/gprofiler/
- ToppGene: http://toppgene.cchmc.org/prioritization.jsp]
- Still need more tools!
- look at OMICtools: http://omictools.com[3]
Links and online tutorials
- Genevestigator website: Introduction to GENEVESTIGATOR?
- Online Genevestigator User manual (PDF)
- Genevestigator Frequently Asked Questions
- Application Note - Data Curation PDF
- Application Note - Data Normalization PDF
- Video tutorial: Introduction to Genevestigator
- Video tutorial: Finding co-regulated genes
- Video tutorial: The Diff-Expression tool
- Video tutorial: The Signature tool
- Video tutorial: The BiClustering tool
- Video tutorial: The Co-Expression tool
- Video tutorial: The RefGenes tool
More Info
References:
- ↑
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) - ↑
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) - ↑ 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) - ↑ http://www.vib.be/en/training/research-training/courses/Pages/Analysis-of-public-microarray-data-using-Genevestigator.aspx
- ↑ https://www.bits.vib.be/index.php/training/125-genevestigator
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