Results: 4

1.
Figure 2

Figure 2. From: A comparative genomics approach to identifying the plasticity transcriptome.

Relative frequency of transcription factor binding sites within promoter regions across species. (A) The percentage of human, mouse, and rat promoters with a predicted CREB binding site. (B) The same as (A), but for zif268. (C) The percent of genes within the homologene dataset showing a CREB or zif268 site, calculated by (# of promoters with a binding site × 100)/(# of human and mouse homologous pairs).

Andreas R Pfenning, et al. BMC Neurosci. 2007;8:20-20.
2.
Figure 1

Figure 1. From: A comparative genomics approach to identifying the plasticity transcriptome.

Activity dependent transcription factor binding sites consensus sequences. The height of the letters is proportional to their frequency in the data used to build the matrix. For instance, a large "A" in position one means that "A" belongs to the most probable consensus for that transcription factor binding site. (A) Consensus sequence given by the transfac CRE-binding matrix V$CREB_01. (B) Consensus sequence given by the transfac zif268 binding matrix V$EGR1_01.

Andreas R Pfenning, et al. BMC Neurosci. 2007;8:20-20.
3.
Figure 3

Figure 3. From: A comparative genomics approach to identifying the plasticity transcriptome.

CREB and zif268 binding sites show strong location specificity. All histograms were created using a bin size of 50 bp. The total number of binding sites in each 50 bp region was divided by the total number of promoters for that dataset. Shown are both human (red) and mouse (blue) and promoters. For the intergenic dataset, the area shown is from -51,200 bp to -50,000 bp relative to transcription start. The mouse dataset is the location of mouse binding sites when the homologous gene also has a binding site of the same type. The human dataset is the location of human binding sites when the homologous gene also has a binding site of the same type. A) Promoters with a CREB binding site are grouped by position relative to transcription start, showing pronounced location specificity within the promoter. (B) The same as (A) but for zif268. (C) The same as (A) but for the conserved CREB targets in the mouse-human homogene dataset. (D) The same as (A) but for the conserved zif268 targets in the mouse-human homogene dataset. The percentage of promoters with a binding site is calculated relative to the total number of homologous pairs.

Andreas R Pfenning, et al. BMC Neurosci. 2007;8:20-20.
4.
Figure 4

Figure 4. From: A comparative genomics approach to identifying the plasticity transcriptome.

Binding site location in CREB/zif268 double hits. Promoter regions for the genes on the line to the left are from -1000 bp to 200 bp relative to transcription start, which is denoted by the arrow. The red blocks above represent CREB binding sites while the green blocks represent zif268 binding sites. Mouse transcription factor binding sites are found on top of the line while human sites are below. A non-alignment method was used to identify promoter regions, so homologous binding sites might not be at the same location. Gene symbols shown are those for mouse. Promoter regions shown are for (A) FBJ osteosarcoma oncogene B/FosB, (B) Jun proto-oncogene related gene d1 (C) v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian), (D) SKI-like, (E) neuronal pentraxin 1, and (F) tropomyosin 4. The targets in the yellow box represent transcription factors.

Andreas R Pfenning, et al. BMC Neurosci. 2007;8:20-20.

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