Difference between revisions of "Sulfiknights DA Week 14"
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==Conclusion== | ==Conclusion== | ||
The data analysis performed produced various graphs showing expression trends and networks that depicted regulation between genes. | The data analysis performed produced various graphs showing expression trends and networks that depicted regulation between genes. | ||
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==Acknowledgements== | ==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. | 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. | ||
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Revision as of 16:31, 7 December 2019
| 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 | ||||||
Contents
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
- Downloaded all STEM software needed found on Week 9.
- 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
- Converted this file into a .txt file
- Ran STEM with this file under these parameters:
- No normalization/add 0
- Spot IDs included in the data file
- Browse: gene_association.sgd.gz
- Selected "X-axis scale should be: Based on real time" in the Interface Options on the All STEM Profiles (1) pop-up window.
- All genelists and GOlists for the significant profiles (9,23,40, and 48) were downloaded and saved.
- 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.
- Copied the gene lists from Profile 9 and 23 and inputted them into
Data and Files
Conclusion
The data analysis performed produced various graphs showing expression trends and networks that depicted regulation between genes.
References
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.
