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Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila

Enrique Blanco1, Miguel Pignatelli14, Sergi Beltran12, Adrià Punset1, Silvia Pérez-Lluch1, Florenci Serras1, Roderic Guigó23 and Montserrat Corominas1*

  • * Corresponding author: Montserrat Corominas mcorominas@ub.edu

  • † Equal contributors

Author Affiliations

1 Departament de Genètica and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Catalonia, Spain

2 Centre de Regulació Genòmica, Parc de Recerca Biomèdica de Barcelona, Dr. Aiguader 88, 08003 Barcelona, Catalonia, Spain

3 Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica - Universitat Pompeu Fabra Barcelona, Catalonia, Spain

4 Current address: Instituto Cavanilles of Biodiversity and Evolutionary Biology, University of Valencia, Apdo 22085, 46071 Valencia, Spain and CIBER of Epidemiology and Public Health (CIBERESP)

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Genome Biology 2008, 9:R134  doi:10.1186/gb-2008-9-9-r134

Published: 10 September 2008

Additional files

Additional data file 1:

Up- and down-regulated genes in the trx microarray.

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Additional data file 2:

General features of the clusters of genes deregulated by TRX.

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Additional data file 3:

Clusters detected using our own clustering approach.

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Additional data file 4:

Clusters detected in random gene sets (gene distribution).

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Additional data file 5:

Clusters detected in random gene sets (gene size).

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Additional data file 6:

Different clusters detected in the genome that are deregulated by several chromatin remodelers.

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Additional data file 7:

Up- and down-regulated genes in the ash2 microarray.

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Additional data file 8:

Average lengths of the deregulated genes on each microarray (clustered or not).

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Additional data file 9:

Clustering analysis in other microarrays of transcription factors.

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Additional data file 10:

Average gene size of deregulated genes in the microarrays analyzed in this study.

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Additional data file 11:

Cumulative distribution Pearson correlation coefficient means in the real and the artificial clusters.

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Additional data file 12:

GO functional annotation of the trx clusters.

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Additional data file 13:

Clusters of genes in the genome associated with similar categories (cuticle/chitin binding).

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Additional data file 14:

Intersection between the trx clusters, the ChIP-on-chip information and the PRE/TRE predictions.

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Additional data file 15:

Chromatin immunoprecipitation using anti-TRX and H3K4me3 specific antibodies to test the binding of TRX to the predicted PRE/TREs in clusters 9 and 25.

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Additional data file 16:

Examples of clusters and transfrags that detect similar patterns of expression.

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Additional data file 17:

Graphical genome-wide representation of the clusters of trx and the HCNEs mapped in several Drosophila species.

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Additional data file 18:

Orthologous genes between D. melanogaster and the other Drosophila species or mosquito.

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Additional data file 19:

The optimal window length to discriminate between real and artificial clusters.

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Additional data file 20:

Alternative overlap analysis among the clusters of genes regulated by different chromatin remodelers (only genes affected in the same way are considered).

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