Sample Analysis

For this example, we continue using the alignment created in Subheading 4. Given the human-chicken and human-opossum alignments, we need to select a region for rVISTA analysis, using the conserved regions shown on the graph as a rough guideline. The double peaks at 127.7 Kbp look like an interesting area to explore, as they are conserved all the way through chicken and opossum. Highlight that area to zoom into it, being careful to select less than 20 Kbp. Once you are zoomed in, click the "I" button to see the alignment details. The link to submit to rVISTA is on the right. Select the human-chicken alignment, and proceed with the submission as described above. Use the recommended threshold matrix cutoff, and select the following factors, which we can reasonably expect to show up given the description of the gene RUNX1 at NCBI and Ensembl: AML, AML1, PEBP, PEA3 (see Note 7). The analysis shows three predicted conserved transcription factor binding sites for the AML1 factor (Fig. 5).

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