Transcript Interactive web tools

Interactive analysis of lists
…on the web
Raymond Ripp
19 février 2013
Data and Tools
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GxDb
ImAnno
Gscope
GO
SM2PH
EvoluCode
…
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/biolo/…
PHP programs
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PipeWork
DoOnlist
HtmlTable
RadarGenerator
StringInteractome
GoGet
CytoscapeWeb
DecoreTree
Example 1 :
a PipeWork to Combine Lists of Genes
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How to combine lists of genes from
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ImAnno sieves (search tool using SQL
queries)
Transcriptomic Expression (GxDb Web
Service)
Diseases related genes (from previously
stored lists)
With Union, Intersection, AnotB, …
Cochlea
Sacculus
Utriculus
sieves
cochlea
sacculus
utriculus
other
ISH
Annotation
Select Store
Transcriptomic
Jax
Ihr
Sanger
All
Select Disease
Diseases
Intersection
Intersection
GenePaintGenes
Information
… more details
EGEcoch
EGEsac
EGEutri
EGEother
key
organ
Cochlea
Sacculus
Utriculus
sieves
Union
Inter
AnotB
BnotA
cadre
Select Store
FromStore
action
action
FromSieves
Jax
Ihr
Sanger
All
UnionInter
AnotBnotA
What to name,descript,entrez,ege,go
display
Union
Inter
AnotB
BnotA
FromStore
Select Disease
Union
Inter
AnotB
BnotA
action
UnionInter
AnotBnotA
GenePaintgenes
HtmlTable
Output
EGEcoch
EGEsac
EGEutri
EGEother
key
organ
Cochlea
Sacculus
Utriculus
sieves
Union
Inter
AnotB
BnotA
cadre
Select Store
FromStore
action
action
FromSieves
Jax
Ihr
Sanger
All
UnionInter
AnotBnotA
What to name,descript,entrez,ege,go
display
Union
Inter
AnotB
BnotA
FromStore
Select Disease
Union
Inter
AnotB
BnotA
action
UnionInter
AnotBnotA
GenePaintgenes
HtmlTable
Output
EGEcoch
EGEsac
EGEutri
EGEother
key
organ
Cochlea
Sacculus
Utriculus
sieves
Union
Inter
AnotB
BnotA
cadre
Select Store
FromStore
action
action
FromSieves
Jax
Ihr
Sanger
All
UnionInter
AnotBnotA
What to name,descript,entrez,ege,go
display
Union
Inter
AnotB
BnotA
FromStore
Select Disease
Union
Inter
AnotB
BnotA
action
UnionInter
AnotBnotA
GenePaintgenes
HtmlTable
Output
ImAnno Gene List
HtmlTable as output of the PipeWork
PipeWork
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… merci à
Laetitia Poidevin
Nicolas Gagnière
Guillaume Berthommier
Example2 : PipeWork ClusterComposition
HtmlTable
From an HtmlTable to DoOnList
DoOnList
DoOnList Help
From DoOnList to RadarGenerator
RadarGenerator
From DoOnList to GO
From DoOnList to StringInteractome
… don’t forget to specify the organism
organism=Mus_musculus
StringInteractome Summary
From DoOnList to EvoluCode
DoOnList Help
From ImAnno to Itol
From Itol to DecoreTree
http://lbgi.fr/fed
Paste your gene list to StringInteractome
Conclusion … and To Do
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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.