BIOL398-04/S15:Jeffrey Crosson Week 12
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- My profile 45 had the most amount of genes in it, so I decided to input this profile's genes into the YEASTRACT database.
- YEASTRACT determined that 24 of the transcription factors had a low enough of a p value.
- Here's a spreadsheet of these transcription factors with the corresponding percent in user set, percent in YEASTRACT, and p value: Excel Spreadsheet
- Only five transcription factors with significant p values appeared in both of our lists.
- We first started with all of the transcription factors that overlapped. Then we added in all of the wild type transcription factors. Then four transcription factors were subtracted from this list to make it contain 30 transcription factors.
- It was difficult determining which transcription factors are significant due to the DeltaCIN5 not having many significant transcription factors. We first started with all of the transcription factors that overlapped. Then we added in all of the wild type transcription factors. Then four transcription factors were subtracted from this list to make it contain 30 transcription factors
- Creating the three candidate gene regulatory networks entailed using different standards to assert relationships. The DNA binding plus expression evidence was the least strict, so it found a connection between all of them. “Binding only” was a little stricter, so it found fewer connection. The DNA binding and expression data required that there was evidence for relatedness in both a DNA binding test and in expression tests, so it had the least amount of connection.
- The strict DNA binding and expression data set had 17 edges and had mostly low in-degrees and diverse out-degrees. This means that it didn't find many connections, as in most transcription factors were affected by a small number of genes. The “binding only” data had similar results but with 67 edges. The in-degrees were smaller, but the out degrees were larger. Several transcription factors affect many other transcription factors, but the number of transcription factors that can affect an individual transcription factor is smaller. The “plus” group was very large, as it had 225 edges. This is a problem, because there are too many connections to make sense of.
- The excel files were formatted and inputted into GRNsight in order to create schematics of the gene networks. The “and” and “binding only” had practical sizes
- We have selected "Binding only" because it is a practical size. “And" is undersized and “plus” is oversized.
- We've added the degree distribution charts and network graphs in our latest iteration of our presentation: PowerPoint Presentation
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