Research
Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila
- † Equal contributors
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)
Genome Biology 2008, 9:R134 doi:10.1186/gb-2008-9-9-r134
Published: 10 September 2008Additional 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).
Format: PDF Size: 12KB Download file
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