Difference between revisions of "Sulfiknights DA Week 14"
Jump to navigation
Jump to search
(→Methods and Results: wrote section) |
(→Purpose: fix) |
||
| Line 2: | Line 2: | ||
==Purpose== | ==Purpose== | ||
| − | + | * To analyze data collected by [https://doi.org/10.1152/physiolgenomics.00236.2006 Thorsen et al.] regarding gene expression changes in response to sulfate exposure through using an ANOVA, running [http://www.cs.cmu.edu/~jernst/stem/ STEM], [http://www.yeastract.com/ YEASTRACT], [https://dondi.github.io/GRNsight/ GRNsight], [http://kdahlquist.github.io/GRNmap/downloads/ GRNmap], and Microsoft Access | |
| + | * To check the efficacy of the work done by [https://doi.org/10.1152/physiolgenomics.00236.2006 Thorsen et al.] | ||
==Methods and Results== | ==Methods and Results== | ||
Revision as of 16:25, 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
