Difference between revisions of "Sulfiknights DA Week 12/13"
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(→Data & Files: added link to excel file) |
(→Organizing Data Sheet: added link, edited) |
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====Organizing Data Sheet==== | ====Organizing Data Sheet==== | ||
#Downloaded data from Thorsen et al. | #Downloaded data from Thorsen et al. | ||
| − | |||
#Changed "Name" to "Standard_ID" in column C. | #Changed "Name" to "Standard_ID" in column C. | ||
| − | #*Names were changed to the standard names by | + | #*Names were changed to the standard names by the [http://www.yeastract.com/formorftogene.php "ORF List <-> Gene List"] tool from YEASTRACT. |
#Changed column headers in each sheet: | #Changed column headers in each sheet: | ||
#*swt = stressed wild type, nswt= nonstressed wild type | #*swt = stressed wild type, nswt= nonstressed wild type | ||
| Line 20: | Line 19: | ||
#*1h, 15m, 30m, 18h = time point (h = hours, m = minutes) | #*1h, 15m, 30m, 18h = time point (h = hours, m = minutes) | ||
#*rn = replicate number (n) | #*rn = replicate number (n) | ||
| + | #Inserted MasterIndex in "GSE6068_setA_family"sheet. | ||
| + | |||
====Calculating p-values==== | ====Calculating p-values==== | ||
Sanity Check: 1068/4785 p-values are less than 0.05 | Sanity Check: 1068/4785 p-values are less than 0.05 | ||
Revision as of 16:09, 25 November 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
Methods & Results
Sample to data relationship table:
- GSE6068_setA_family - swt vs nswt 1mM @ 1 hr (6 replicates); 15 min, 30 min, 18 hrs (3 replicates each)
- GSE6129_set0_family - swt vs nswt 1mM @ 1hr; 6 replicates
- GSE6129_set1_family - swt vs nswt .2mM @ 1 hr, 15 min, 30 min, 18 hr; 3 replicates each
- GSE6129_set2_family - sYAP4 vs swt .2mM AND 1 mM each @ 1 hr, 3 replicates each
- GSE6129_set3_family - sMET4 vs swt .2mM AND 1 mM each @ 1 hr, 3 replicates each
ANOVA
Organizing Data Sheet
- Downloaded data from Thorsen et al.
- Changed "Name" to "Standard_ID" in column C.
- Names were changed to the standard names by the "ORF List <-> Gene List" tool from YEASTRACT.
- Changed column headers in each sheet:
- swt = stressed wild type, nswt= nonstressed wild type
- 1mM, 0.2mM = concentration of As(III) at which the cell was exposed
- 1h, 15m, 30m, 18h = time point (h = hours, m = minutes)
- rn = replicate number (n)
- Inserted MasterIndex in "GSE6068_setA_family"sheet.
Calculating p-values
Sanity Check: 1068/4785 p-values are less than 0.05
Data & Files
Conclusion
Acknowledgments
References
- Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006
