Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster

doi:10.1186/1471-2164-10-9

BMC Genomics

Volume 10

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Research article

Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster

Qianqian Zhu¹^,2 and Marc S Halfon¹^,3^,4^,5

¹Department of Biochemistry, Buffalo, NY 14214, USA

²Department of Biostatistics, Buffalo, NY 14214, USA

³Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14214, USA

⁴New York State Center of Excellence in Bioinformatics and the Life Sciences, Buffalo, NY 14203, USA

⁵Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA

author email corresponding author email

BMC Genomics 2009, 10:9doi:10.1186/1471-2164-10-9


Published:	7 January 2009

Additional files

Additional file 1:

Figures S1 and S2. Mononucleotide distributions of the three groups of promoters when using "high quality" fly promoters (S1A), cap-supported fly promoters (S1B) and human promoter sets (S2).

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Additional file 2:

Tables S1-S4. Table S1: Drosophila promoter motifs used in this study; Table S2: Motif preferences when using different motif position requirements; Table S3: Motif preferences when using regular expressions versus position weight matrices to represent motifs; Table S4: Human promoter motifs used in this study.

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Additional file 3:

Promoter motif coordinates from our primary study. This file contains all of the mapped motifs from our primary study formatted for upload to the Generic Genome Browser (GBrowse) as a custom annotation.

Format: TXT Size: 432KB Download file

Additional file 4:

Promoter motif coordinates using "combined range". This file contains all of the mapped motifs using the motif definitions and position requirements "combined range" formatted for upload to the Generic Genome Browser (GBrowse) as a custom annotation.

Format: TXT Size: 408KB Download file

Additional file 5:

Promoter motif coordinates from Patser. This file contains all of the mapped motifs using Patser, as described in the text, formatted for upload to the Generic Genome Browser (GBrowse) as a custom annotation.

Format: TXT Size: 817KB Download file

Additional file 6:

Figure S3. Motif dissimilarity distributions between alternative promoters of the same gene and between neighboring unique promoters.

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Additional file 7:

neighboring single-promoter genes. This file contains the names and coordinates of the pairs of neighboring single-promoter genes used for the analysis presented in Table 5 and Figure 3.

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Additional file 8:

Figure S4. Distribution of the number of mapped motifs in individual promoters.

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Additional file 9:

Figure S5. Histogram of distances between alternative TSSs for the same gene in the fly genome when all promoters in the genome (A) or only cap-supported promoters (B) were considered.

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