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Discover de novo motifs

• Select Motif discovery Discovery from the Peak Analysis section of the ChIP-Seq workflow
• Select Discover de novo motifs
• Select OK

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In this case, the motif finder discovered a motif in the NRSF-enriched regions that is 16 base pairs in length. The height of each position is the relative entropy (in bits) and indicates the importance of a base at a particular location in the binding site.

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1. Counts gives the summed counts for each base call across all occurrences of the motif in the region list as {A, C, G, T} 

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1-4. chromosome, start, stop, strand give the position

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Two spreadsheets are created, similar to the spreadsheets in the de novo motif discovery, the motif_summary (MotifSearch) spreadsheet (Figure 67) and the motif_instances (MotifSearch.instance) spreadsheet. 

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In the MotifSearch spreadsheet, each motif used in the motif search is shown. The columns detail the results of the search for each motif that was found in the reads. 

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As you can see, REST, which is another name for NRSF, is near the top of the list as one of the most significantly over-represented motifs (Figure 67). This motif agrees with the motif found in the de novo motif detection step. Interestingly, other motifs appear a significant number of times in the ChIP-Seq peaks and may represent possible co-factors or regulators. 

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• Select the motif_instances spreadsheet in the spreadsheet tree 
• Right-click the 5. Motif Name column 
• Select Find / Replace / Select... from the pop-up menu (Figure 78)
  
  

• Set Find What: to REST
• Select By Columns for Search: 
• Select Only in column with 5. Motif Name selected form the drop-down menu
• Select Select All (Figure 89)
  
  

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• Right-click on the first highlighted row visible; in this example, we see row 13196 
• Select Filter Include from the pop-up menu (Figure 910)
  
  

The spreadsheet will now include 2098 rows and a black and yellow bar will appear on the right-hand side of the spreadsheet (Figure 1011). The black and yellow bar is a filter indicator showing the fraction of the spreadsheet currently visible as yellow and the filtered fraction as black. 

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Neuwald, A. F., Liu, J.S., & Lawrence, C.E. (1995). Gibbs motif sampling: detection of outer membrane repeats (Vol. 4). Protein Science.