Sulfiknights DA Week 14

Sulfiknight Links
BIOL Databases Main Page	Sulfiknights: Project Overview Page	Final Project Deliverables Requirements	Sulfiknights: Final Project Deliverables	Members	Project Manager & Quality Assurance: Naomi Tesfaiohannes	Quality Assurance: Joey Nimmers-Minor	Data Analysis: Ivy-Quynh Macaraeg & Marcus Avila	Designer: DeLisa Madere
				Assignment Pages	Week 11	Week 12/13	Week 15

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Purpose

• To analyze data collected by Thorsen et al. regarding gene expression changes in response to sulfate exposure through using an ANOVA, running STEM, YEASTRACT, GRNsight, GRNmap, and Microsoft Access
• To check the efficacy of the work done by Thorsen et al.

Methods and Results

Loading Data into STEM

1. Downloaded all STEM software needed found on Week 9.
2. Deleted the "1080" data column from the "swtVnwt_1mM_stem" sheet found in the Thorsen Data Excel File.
   • This was done so that the profile graphs were clearer
3. Converted this file into a .txt file
4. Ran STEM with this file under these parameters:
   • No normalization/add 0
   • Spot IDs included in the data file
   • Browse: gene_association.sgd.gz
5. Selected "X-axis scale should be: Based on real time" in the Interface Options on the All STEM Profiles (1) pop-up window.
6. All genelists and GOlists for the significant profiles (9,23,40, and 48) were downloaded and saved as .txt files.
   • Profiles 9 and 23 were colored red to show clusters that were involved in down-regulation.
   • Profiles 40 and 48 were colored green to show clusters that were involved in up-regulation.

Creating regulatory networks with YEASTRACT

1. Copied the gene lists from Profile 9 and 23.
2. Inputted this list into the YEASTRACT database and under the "Rank by TF".
3. Took the first 17 significant transciption factors and put them into both boxes of the Generate Regulation Matrix page.
   • CSV file that was generated was converted into an Excel file.
4. File was delimited and organized so that "p"s were deleted, everything was captalized, and the regulatees and regulators were alphabetized and in the same order.
5. Position A1 was changed to the text: "rows genes affect/cols genes controlling".
6. We deleted transcription factors that were not connected to others and/or only connected to itself.
7. Sheet was named "network", saved, and inputted into the GRNsight home page.

Steps 1-7 were repeated with the genes from Profiles 40 and 48. In the end, we had two networks and two GRNsight matrices (black and white).

Conclusion

The data analysis performed produced various graphs showing expression trends and networks that depicted regulation between genes.

Acknowledgements

We would like to thank User:Kdahlquist for helping with this investigation. Except for what is noted above, this individual journal entry was completed by the member of team Sulfiknights and not copied from another source.