Difference between revisions of "Emmatyrnauer Week 15"

Revision as of 00:06, 15 December 2017

Electronic Notebook

In week 14 I produced a gene regulatory network utilizing Yeastract and GRNsight. However, this regulatory network was too large. To trim the network, I removed transcription factors one by one, each time visualizing the newly trimmed list in GRNsight. I had to visualize the trimmed network in GRNsight to ensure that there were no loose end/floating transcription factors (i.e. transcription factors that were not connected to any others in the network). The process of removal is documented in Media: REGULATIONMATRIXFINAL_ET.zip, with the final version being #5 (this media file has also been linked to on Emmatyrnauer Week 14 as it allowed Dr. Dahlquist to check over the network and provide me with the initial unweighted input file for GRNsight ( 17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx) on my user talk page. When opened in GRNsight, this input file produced Figure 1. In this figure, you are able to visualize the presence of interactions between genes. However, the nature of these interactions cannot be understood. That is, the magnitude of the interactions and whether or not they are induction or repression. So, Matlab was utilized to create a weighted network file. This file was opened in GRNsight and produced Figure 2. Pink arrows indicate repression while blue lines with bars indicate repression. It appears that most interactions are repression of other genes and that MSN2 is largely responsible for inhibiting many other genes.

Figure 1. Unweighted network

Figure 2. Weighted network

Acknowledgements

1. Lights, Camera, InterACTION! for collaboration in the creation of the group presentation and paper.
2. Dr. Dahlquist for assisting in the alteration of the significant genes excel spreadsheet to create an input file for Matlab (including the deletion and insertion of genes).
3. Yeastract for determining the most significant transcription factors in profile 45 of wild type data.
4. Matlab for creating the output file which was used to create weighted gene regulation map.
5. GRNsight for generation of gene map (both weighted and unweighted).
6. While I worked with the people and programs noted above, this individual journal entry was completed by me and not copied from another source.

References

1. YEASTRACT. Retrieved December 7, 2017, from http://www.yeastract.com/formgenerateregulationmatrix.php
2. GRNsight (2017) Retrieved December 7, 2017, from http://dondi.github.io/GRNsight/
3. Matlab. Retrieved December 7, 2017, from LMU's computer lab (https://www.mathworks.com/products/matlab.html)

Links

1. My User Page
2. List of Assignments
   • Week 1
   • Week 2
   • Week 3
   • Week 4
   • Week 5
   • Week 6
   • Week 7
   • Week 8
   • Week 9
   • Week 10
   • Week 11
   • Week 12
   • no Week 13
   • Week 14
   • Week 15
3. List of Journal Entries
   • Emmatyrnauer Week 1
   • Emmatyrnauer Week 2
   • Emmatyrnauer Week 3
   • Emmatyrnauer Week 4
   • Emmatyrnauer Week 5
   • Emmatyrnauer Week 6
   • Emmatyrnauer Week 7
   • Emmatyrnauer Week 8
   • Emmatyrnauer Week 9
   • Emmatyrnauer Week 10
   • Emmatyrnauer Week 11
   • Emmatyrnauer Week 12
   • no Week 13
   • Emmatyrnauer Week 14
   • Emmatyrnauer Week 15
4. List of Shared Journal Entries
   • Class Journal Week 1
   • Class Journal Week 2
   • Class Journal Week 3
   • Class Journal Week 4
   • Class Journal Week 5
   • Class Journal Week 6
   • Class Journal Week 7
   • Class Journal Week 8
   • Class Journal Week 9
   • Class Journal Week 10
   • Group Journal Week 11
   • Group Journal Week 12
   • no week 13
   • Group Journal Week 14 (executive summary)
   • Group Journal Week 14 (executive summary)
   • Group Journal Week 15 (executive summary)