How to analyse list of genes

Raymond Ripp

19 février 2013

Data and Tools

GxDb ImAnno Gscope GO SM2PH EvoluCode …

/biolo/… PHP programs

PipeWork DoOnlist HtmlTable RadarGenerator StringInteractome GoGet CytoscapeWeb DecoreTree

PipeWork to Combine Gene Lists

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, …

sievesCochleaSacculusUtriculus

Select Storecochleasacculusutriculus

other

Select DiseaseJaxIhr

SangerAll

ISHAnnotation

Intersection

GenePaintGenesInformation

Intersection

Transcriptomic

Diseases

… more details

Output

cadre

sievesCochleaSacculusUtriculus

action

UnionInter

AnotBBnotA

organ

key

action

UnionInter

AnotBBnotA

Select StoreEGEcochEGEsacEGEutri

EGEother

action

UnionInter

AnotBBnotA

Select DiseaseJaxIhr

SangerAll

What to display

name,descript,entrez,ege,go

FromSieves

UnionInterAnotBnotA

GenePaintgenes

UnionInterAnotBnotA

HtmlTable

FromStore

FromStore

ImAnno Gene List

PipeWork … merci à

Laëtitia Poidevin Nicolas Gagnière Guillaume Berthommier

organism=Mus_musculus

http://lbgi.fr/fed

Conclusions … and To Do

It works … The user has his own lists The analysis tools create new lists It allows to combine different web sites and systems

We have to add more and more tools. Test it on real cases

We have to : Organize user’s data Allow multi sessions Add new functionalities Use it intensively.

merci.