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Open Access Research article

Rigorous and thorough bioinformatic analyses of olfactory receptor promoters confirm enrichment of O/E and homeodomain binding sites but reveal no new common motifs

Janet M Young1*, Ralf M Luche12 and Barbara J Trask1

Author Affiliations

1 Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA

2 Present address: Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA

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BMC Genomics 2011, 12:561  doi:10.1186/1471-2164-12-561

Published: 15 November 2011

Additional files

Additional file 1:

Table listing olfactory receptor genes and pseudogenes in the July 2007 mouse genome assembly. See Methods for details of how gene names were determined.

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Additional file 2:

Table listing TSS locations and data sources. This table shows all TSS locations we collected from a high-throughput RACE study [20], our hybridization-based cDNA screen [13] and various other RACE experiments performed on smaller numbers of ORs [6,14,17,18,52,85-87]. For some ORs, more than experiment defines a TSS (so there are multiple rows for some genes in this table). The "Best TSS?" column indicates whether each defined TSS is the most upstream one for that gene ("Best"), or lies downstream of another TSS for the same gene ("NotBest"). The most upstream TSS for each gene is included in Additional File 1 and was used in our promoter analyses. * Gene names are given where the TSS location was derived from RACE experiments (excluding the high-throughput RACE experiments of Michaloski et al.).

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Additional file 3:

Figure showing that most O/E sites predicted using MatInspector's less stringent parameters are evolutionarily conserved. The solid gray line shows all mouse O/E sites predicted using MatInspector's less stringent parameters. For reference we include a dotted gray line showing all mouse O/E sites predicted using MatInspector's default parameters. As in Figure 1, coverage is calculated as the proportion of promoter sequences containing a predicted O/E binding site at each base-pair, averaged over 20-bp windows, sliding along promoters 1 bp at a time. In panel A, the colored lines show predicted mouse O/E sites that remain after we apply an evolutionary "filter" to MatInspector predictions on a multiple sequence alignment (see Methods). For example, the red line shows mouse O/E sites that have overlapping O/E sites in a set of mammals with tree length of at least 1.5. Note that the conservation filter removes many of the O/E sites far away from the TSS and selects for likely functional sites near the TSS. In panel B, we explore the effect of allowing various amounts of "slide" (see Methods), where sites in other species are no longer required to overlap but could be various distances away, accounting for evolutionary "turnover" [62].

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Additional file 4:

Figure showing enrichment of transcription factor binding sites 200 bp before TSS using less stringent MatInspector parameters. These plots follow the same layout as those in Figure 2 but use transcription factor site predictions made using MatInspector with less stringent parameters (see Methods).

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Additional file 5:

Table summarizing statistical tests on matrix families for 200-bp promoter region (default MatInspector parameters). Results of our statistical tests for enrichment and conservation for all matrix families after masking O/E sites and TATA boxes using default MatInspector parameters. See legend to Table 1.

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Additional file 6:

Table summarizing statistical tests on matrix families for 200-bp promoter region (less stringent MatInspector parameters). Results of our statistical tests for enrichment and conservation for all matrix families after masking O/E sites and TATA boxes using less stringent MatInspector parameters. See legend to Table 1.

Format: XLSX Size: 45KB Download file

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Additional file 7:

Summary of statistical tests for 500-bp promoter region. See legend to Table 1. This table gives equivalent statistics for a larger putative promoter region comprising 500bp before the TSS. Binomial tests here show comparison with the preceding 500-bp region.

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Additional file 8:

Table summarizing statistical tests on matrix families for 500-bp promoter region (default MatInspector parameters). See legend to Additional File 5.

Format: XLSX Size: 45KB Download file

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Additional file 9:

Table summarizing statistical tests on matrix families for 500-bp promoter region (less stringent MatInspector parameters). See legend to Additional File 6.

Format: XLSX Size: 46KB Download file

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Additional file 10:

Table summarizing statistical tests on individual matrices for 200-bp promoter region (default MatInspector parameters). Results of our statistical tests for enrichment and conservation for individual matrices after masking O/E sites and TATA boxes using less stringent MatInspector parameters. See legend to Table 1. In addition, for selected matrices, we obtained gene symbols of the corresponding transcription factor(s) (using MatBase and/or the Mouse Genome Database: [72]), and used gene symbols to query RNA-seq data generated from mature olfactory neurons and a mix of immature neurons and precursors [41]. We provide here the gene symbol and two numbers representing expression levels in OMP+ cells (mature olfactory neurons) and NGN+ cells (immature olfactory neurons and precursors), respectively (see Methods).

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Additional file 11:

Table summarizing statistical tests on individual matrices for 200-bp promoter region (less stringent MatInspector parameters). Results of our statistical tests for enrichment and conservation for individual matrices after masking O/E sites and TATA boxes using less stringent MatInspector parameters. See legend to Table 1 and Additional File 10.

Format: XLSX Size: 136KB Download file

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Additional file 12:

Table summarizing statistical tests on individual matrices for 500-bp promoter region (default MatInspector parameters). See legend to Additional File 10.

Format: XLSX Size: 138KB Download file

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Additional file 13:

Table summarizing statistical tests on individual matrices for 500-bp promoter region (less stringent MatInspector parameters). See legend to Additional File 11.

Format: XLSX Size: 137KB Download file

Open Data