1 / 35

Interactive Gene List Analysis and Combination Tools for Biological Research

This document discusses innovative web-based tools and techniques for combining and analyzing gene lists from various sources, including ImAnno, GxDb, and Infection-related databases. It demonstrates how to utilize PipeWork, DoOnList, and radar generation tools to create comprehensive analyses tailored to specific organisms, such as Mus musculus. Users can work with new and existing gene lists, utilizing intersection, union, and other operations to explore data related to diseases and gene functions. The platform allows for storage, restoration, and downloading of results, facilitating extensive and collaborative research.

eshe
Download Presentation

Interactive Gene List Analysis and Combination Tools for Biological Research

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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. ImAnno Gene List

  7. HtmlTable as output of the PipeWork

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

  9. Example2 : PipeWork ClusterComposition

  10. HtmlTable

  11. From an HtmlTable to DoOnList

  12. DoOnList

  13. DoOnList Help

  14. From DoOnList to RadarGenerator

  15. RadarGenerator

  16. From DoOnList to GO

  17. From DoOnList to StringInteractome

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

  19. StringInteractomeSummary

  20. From DoOnList to EvoluCode

  21. DoOnList Help

  22. From ImAnno to ItolFrom Itol to DecoreTree

  23. http://lbgi.fr/fed

  24. Paste your gene list to StringInteractome

  25. 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.

More Related