Text Box: G E N E R A T O R
Text Box:  
Text Box: M A I N P A G E
Text Box: G E N E l I s t  R e s e a r c h  A i m e d  T h e m e- d I s c o v e r y  e x e c u t O R

 

 

 

 

 

Background: High throughput methods of modern molecular biology produce vast amounts of data in a form of gene lists that are difficult to interpret. Existing methods analyse a list as one entity albeit often it is comprised of multiple gene groups associated with separate biological functions. Therefore it seems reasonable to see if gene groups with different functionality can be found from the analysed gene list.

Results: In order to analyse this division we have developed a method that clusters genes to the groups with homogenous functionalities. Method uses Non-negative Matrix Factorization to create several clustering results with varying number of clusters. Obtained clustering results are used to create a simple graphical presentation of the functional groups enriched in gene list. We demonstrate its performance on various data sets and show results that would be undetected with competing methods. Comparison also shows that our method creates a more simplified view that discards less informative classes from the results.

Conclusion: Presented method and associated software should turn useful specially when analysing larger gene lists.

 FILES

1

Read instructions carefully

2

For Full Edition:

Install and run MySQL and driver

 

More information about MySQL open source database:

http://www.mysql.com

 

3

Install one of the program clients

 

  • Full Edition 1.02b

    • GO version: March 2005.

    • Species: Human, mouse, rat, zebrafish, fruit fly, C.elegans, yeast, rice, arabidopsis thaliana.

    • Size: 68 MB as zipped.

  • Full Edition 1.01 (recommended version)

    • GO version: April 2004. USED IN THE PUBLICATION.

    • Species: Human, mouse, rat, zebrafish, fruit fly, C.elegans, yeast, rice, arabidopsis thaliana.

    • Size: 63 MB as zipped.

  • Limited Edition 1.01

    • No database. Data import from matrices.

    • Size: 7 MB as zipped.

GENERATOR is released under Open Source licence. Source code can be requested from the authors by email.

4

Try example datasets

Gene lists for yeast mutation datasets:

Data is taken from:

Thorpe GW, Fong CS, Alic N, Higgins VJ, Dawes IW: Cells have distinct mechanisms to maintain protection against different reactive oxygen species: oxidative-stress-response genes. Proc Natl Acad Sci U S A 2004, 101(17):6564-6569.

Corresponding matrices:

 

5

Read the publication

Pehkonen P., Wong G. and Törönen P.: Theme discovery from genelists for identification and viewing of multiple functional groups. BMC Bioinformatics 2005, 6:162.

Petri Pehkonen

Laboratory of Functional Genomics and Bioinformatics

Department of Neurobiology

A.I.Virtanen Institute for Molecular Sciences

University of Kuopio

P.O.B. 1627, Kuopio 70211 FINLAND

Phone (+358)17 162036

E-mail  firstname.lastname@uku.fi

Petri Törönen

Department of Neurobiology

A.I.Virtanen Institute for Molecular Sciences

University of Kuopio

P.O.B. 1627, Kuopio 70211 FINLAND

Phone (+358)17 162036

E-mail  lastname@hytti.uku.fi