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Interactive Analysis of Gene Lists with Online Tools

This guide provides comprehensive insights into the interactive analysis of gene lists using various web-based tools. It details the use of PipeWork to combine gene lists, such as those derived from ImAnno searches and transcriptomic data, while involving operations like union and intersection for gene selection based on disease relevance. The document discusses functionalities of tools like GxDb, DoOnList, and the StringInteractome, facilitating users in managing their data across different platforms. Practical examples illustrate how to effectively use these tools for biological data analysis.

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Interactive Analysis of Gene Lists with Online Tools

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  1. Interactive analysis of lists…on the web Raymond Ripp 19 février 2013

  2. Data and Tools • GxDb • ImAnno • Gscope • GO • SM2PH • EvoluCode • … • /biolo/… • PHP programs • PipeWork • DoOnlist • HtmlTable • RadarGenerator • StringInteractome • GoGet • CytoscapeWeb • DecoreTree

  3. Example 1 : a PipeWork to Combine Lists of Genes • How to combine lists of genes from • ImAnno sieves (search tool using SQL queries) • Transcriptomic Expression (GxDb Web Service) • Diseases related genes (from previously stored lists) • With Union, Intersection, AnotB, …

  4. Cochlea Sacculus Utriculus cochlea sacculus utriculus other sieves Select Store ISH Annotation Jax Ihr Sanger All Transcriptomic Select Disease Intersection Diseases Intersection GenePaintGenes Information … more details url

  5. Output EGEcoch EGEsac EGEutri EGEother Select Store Cochlea Sacculus Utriculus key Union Inter AnotB BnotA sieves Union Inter AnotB BnotA organ action FromStore cadre action FromSieves Jax Ihr Sanger All Select Disease Union Inter AnotB BnotA UnionInter AnotBnotA action FromStore name,descript,entrez,ege,go What to display UnionInter AnotBnotA GenePaintgenes HtmlTable url

  6. Output EGEcoch EGEsac EGEutri EGEother Select Store Cochlea Sacculus Utriculus key Union Inter AnotB BnotA sieves Union Inter AnotB BnotA organ action FromStore cadre action FromSieves Jax Ihr Sanger All Select Disease Union Inter AnotB BnotA UnionInter AnotBnotA action FromStore name,descript,entrez,ege,go What to display UnionInter AnotBnotA GenePaintgenes HtmlTable url

  7. Output EGEcoch EGEsac EGEutri EGEother Select Store Cochlea Sacculus Utriculus key Union Inter AnotB BnotA sieves Union Inter AnotB BnotA organ action FromStore cadre action FromSieves Jax Ihr Sanger All Select Disease Union Inter AnotB BnotA UnionInter AnotBnotA action FromStore name,descript,entrez,ege,go What to display UnionInter AnotBnotA GenePaintgenes HtmlTable url

  8. ImAnno Gene List

  9. HtmlTable as output of the PipeWork

  10. PipeWork … merci à • Laetitia Poidevin • Nicolas Gagnière • Guillaume Berthommier

  11. Example2 : PipeWork ClusterComposition

  12. HtmlTable

  13. From an HtmlTable to DoOnList

  14. DoOnList

  15. DoOnList Help

  16. From DoOnList to RadarGenerator

  17. RadarGenerator

  18. From DoOnList to GO

  19. From DoOnList to StringInteractome

  20. … don’t forget to specify the organism organism=Mus_musculus

  21. StringInteractomeSummary

  22. From DoOnList to EvoluCode

  23. DoOnList Help

  24. From ImAnno to ItolFrom Itol to DecoreTree

  25. http://lbgi.fr/fed

  26. Paste your gene list to StringInteractome

  27. Conclusion … and To Do • It works … • The user can start with his own lists • The analysis tools create new lists • It allows to combine different web sites and systems • The user can store, restore and download his data • Test it on real cases We have to : • Organize user’s data • Allow multi sessions • Add new functionalities • Use it intensively. merci.

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