Aporras1 Individual Assessment and Reflection
User page: Antonio Porras
Assignment page: Deliverables Page
Contents
Individual Assessment and Reflection
Statement of Work
- Describe exactly what you did on the project.
- As data analyst I was responsible for performing statistical analysis on dZAP1 expression data provided by Dr. Dahlquist's lab. During Week 8 I completed the ANOVA test along with calculating Benjamini-Hochberg corrected p value and the Bonferroni-corrected p-value. The first calculation was less stringent compared to the Bonferroni but both were useful in terms of improving the confidence in the data. The precise steps and outline of what I completed can be found in my Aporras1_Week_8 journal.
Moving into Week 10, I performed STEM high level analysis on the ANOVA data in order to generate gene clusters which presented similar expression over the course of the experiment. Seven significant clusters were generated and the GOlists & genelists were saved and uploaded to the wiki for later analysis. I read and interpreted 6 GOlist terms found in the GOlist of Profile 22 and attempted to understand why the cell would be changing expression in genes associated with certain cell processes. The precise steps and outline of what I completed can be found in my Aporras1_Week_10 journal.
In Week 11, I worked alongside Quinn Lanners to perform a literature search on yeast and cold shock to gain brief exposure to journal articles in this area of research and search engine qualities. The precise steps and outline can be found in my Aporras1_Week_11 journal. The following week Quinn Lanners and I did more in-depth research on the specific journal article: Genome-wide analysis of the yeast transcriptome upon heat and cold shock (Becerra et al., 2003). We outlined the introduction, methods, procedure, analysis tools, and overall findings of the article before creating and presenting a presentation to the class which can be found in my Aporras1_Week_12 journal along with the specific outline and approach to interpretation of their data.
In Week 14 and Week 15 I continued work from the Week 10 data analysis and selected profile 22 of dZAP1 from STEM analysis. I then generated a list of significant transcription factors which targeted genes within the genelist provided by STEM and further used those transcription factors to create a regulatory network. This network was actually determined to be too large and Dr. Dahlquist trimmed down the network to 15 transcription factors. The network was then put into GRNsight to visualize the regulation pathways. MATLAB was also used to generate an output which would allow for GRNsight to display the direction of regulation and the magnitude with colors and bold/thin regulation arrows. A more detailed outline for the process can be found in my Aporras1_Week_14 journal.
Once I completed all the analysis, I then put the data onto the deliverables page, presentation, and the final paper along with my analysis. These files can be found in JASPAR_the_Friendly_Ghost_Final_Deliverables. A more detailed outline for the process can be found in my Aporras1_Week_15 journal.
Assessment of Project
- Give an objective assessment of the success of your project workflow and teamwork.
- What worked and what didn't work?
- What would you do differently if you could do it all over again?
- Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
- Content: What is the quality of the work?
- Organization: Comment on the organization of the project and of your group's wiki pages.
- Completeness: Did your team achieve all of the project objectives? Why or why not?
Reflection on the Process
- What did you learn?
- With your head (biological or computer science principles)
- With your heart (personal qualities and teamwork qualities that make things work or not work)?
- With your hands (technical skills)?
- What lesson will you take away from this project that you will still use a year from now?
Acknowledgements
- Copied the structure of the sections in my assessment and reflection from the Deliverables Page.
