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1.
Figure 8

Figure 8. From: Bioinformatic identification of novel putative photoreceptor specific cis-elements.

Predicted rod (left) and cone (right) enriched motifs in the same format as figure 6. The rod motif is similar in sequence and mean position to the central portion of an initiator element, and the cone to a TATA box.

Charles G Danko, et al. BMC Bioinformatics. 2007;8:407-407.
2.
Figure 1

Figure 1. From: Bioinformatic identification of novel putative photoreceptor specific cis-elements.

A block diagram of the iterative alignment/modular motif selection (IAMMS) algorithm used to identify putative functional sites in photoreceptor promoter regions. Boxes represent the input/output of each successive step. Arrows show flow. Circles show the application of a given filter.

Charles G Danko, et al. BMC Bioinformatics. 2007;8:407-407.
3.
Figure 7

Figure 7. From: Bioinformatic identification of novel putative photoreceptor specific cis-elements.

Comparison of rod (top) and cone (bottom) specific predictions made by IAMMS to those made by either DME (yellow), BioProspector (blue), or both DME and BioProspector (orange). For each prediction, the consensus sequence is given using IUPAC ambiguity codes (given in the legend). The following columns represent the ratio of rod to cone occurrences, the E-value of cell-specificity, the mean occurrence position in the promoter relative to the transcription start site, the mean cross-species conservation score, and similarity to any well-known transcription factor binding sites.

Charles G Danko, et al. BMC Bioinformatics. 2007;8:407-407.
4.
Figure 2

Figure 2. From: Bioinformatic identification of novel putative photoreceptor specific cis-elements.

3D histogram representing features of potential motifs after the iterative alignment. The vertical and horizontal axis plot the number of non-overlapping occurrences of a motif, and the motif length in nucleotides (nt), respectively. Color shows the number (on a log-10 scale) of motifs with the given parameters. The box shows the approximate area that is likely to contain functional motifs. The circle shows the region containing the motif sample in Fig. 3A. Longer motifs (> 20 bp) are longer simple or interspersed repeats.

Charles G Danko, et al. BMC Bioinformatics. 2007;8:407-407.
5.
Figure 6

Figure 6. From: Bioinformatic identification of novel putative photoreceptor specific cis-elements.

Predicted rod (left) and cone (right) enriched motifs. Notations are the same as figure 3. Cross-species alignments for Pde6b, Rho (left), Cnga3, and Opn1mw (right) occurrences are shown on the bottom. All occurrences are highly conserved across species (CSCS -1.66, -1.87, -0.93, and -1.79). The rod-specific prediction is similar to the known rod-motif NRE. The cone-specific motif contains a previously known binding site (ROP2) for which it predicts additional occurrences. Non-photoreceptor occurrences have been removed for simplicity (See additional files 1 and 2).

Charles G Danko, et al. BMC Bioinformatics. 2007;8:407-407.
6.
Figure 4

Figure 4. From: Bioinformatic identification of novel putative photoreceptor specific cis-elements.

Highest scoring rod (left) and cone (right) enriched motifs returned after statistical annotation in IAMMS step 3 (position independent) and IAMMS step 5 (position dependant). From the left, columns give the motif logo, the fraction of rod/cone specific occurrences, cell-specificity E-value, mean location relative to the transcription start site (bp), mean phylogenetic conservation score, and similarity to known motifs. The table is sorted based on the fraction of cell-specific sequence (E-value). Note that predictions with similar core sequences are represented by the prediction with the highest E-value in figure 4. All predictions are presented individually in figure 7.

Charles G Danko, et al. BMC Bioinformatics. 2007;8:407-407.
7.
Figure 3

Figure 3. From: Bioinformatic identification of novel putative photoreceptor specific cis-elements.

Example of cone (A) and rod (B) enriched DNA motifs after statistical annotation. Columns from left to right give gene MGI Symbol, cell-specific expression patterns (C, cone; R, rod; background matches are removed for this figure), start position of motif occurrence relative to the transcription start site, strand relative to the transcription start site (+1), consensus sequence (shown on the top), and cross-species conservation score (see methods). Occurrences are sorted by distance from transcription start site. The cone motif (A) is similar to a known binding site (RXR). The rod motif (B) is similar to the c-Myb binding site. For both motifs, non-photoreceptor occurrences (n = 2, 9 for A and B, respectively) have been removed for simplicity.

Charles G Danko, et al. BMC Bioinformatics. 2007;8:407-407.
8.
Figure 5

Figure 5. From: Bioinformatic identification of novel putative photoreceptor specific cis-elements.

(A) Occurrences of a sample ambiguous motif (triangles) analyzed using position cluster discovery. The horizontal axis represents position relative to the putative transcription start site. The vertical position of occurrences was offset to ease viewing. Position clusters (ovals) were identified using agglomerative hierarchical clustering for all occurrences of each motif in the 2 kbp upstream region identified. Clusters with occurrences in the first 400 bp relative to the transcription start site were evaluated for cell-specificity. In this case, the cluster of occurrences nearest the transcription start site is cone-enriched. A second cluster between -250 and -500 is entirely ambiguous. The numbers kr, kc, and kn reflect the number of rod, cone, and background promoters that contain the motif. (B-C) Identification of cell-specific motifs among position-enriched clusters by statistical annotation. The vertical and horizontal axes plot the fraction of rod (B) or cone (C) promoters against the total number of promoters that contain at least one occurrence of a putative motif. Colors are assigned by the number of motifs with a given fraction (log-10 scale). The shaded region represents groups chosen using a p < 0.005 cutoff threshold.

Charles G Danko, et al. BMC Bioinformatics. 2007;8:407-407.

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