STEM-Away

Final Project

Austin Yang

About Me!

1. Rising 11th grade student at high school in New Jersey
2. Interests
1. Biotechnology, Biomathematics, Biophysics, Bioinformatics
2. Journalism
3. Graphic Design
4. Tennis
5. Double Bass
3. Why did I join stemAWAY?
• Provided platform to explore bioinformatics more
• Passionate and kind community

Research Background

• 1 research paper
• Effects of various poisons on cellular respiration and their societal implications

• First research experience using computer science
• Really tough at first, especially learning new things
• Often lost, but tried to persevere
• Still not perfect (my plots, diagrams, and analysis skills are still quite faulty), but willing to do more bioinformatics research in the future!

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Main Questions and Hypothesis

• The upregulation or downregulation of what genes were primarily responsible for the development of lung cancer?
• Hypothesis: Lung cancer is due to a downregulation of a regulatory gene or protein, causing uncontrollable division
• Little knowledge of lung cancer - based hypothesis off of breast cancer

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Materials and Methods Used

• Materials
• GSE21369, GSE27716, GSE37768, GSE24206
• Database of expression of certain genes, as well as their diagnosis
• QC, normalization, batch correction
• rma() function - performs qc, normalization, and batch correction according to RMA method
• Confirmed results with pipeline learned in internship

Results/Analysis

• KEGG Plot and GO Plot
• Analysis:
• GO plot: Cell Adhesion Molecule Binding upregulated, protein N-terminus binding downregulated
• KEGG plot: Involved genes most similar to Amyotrophic lateral sclerosis and Alzheimer’s Disease
• First time analyzing GO or KEGG plots, so unsure if analysis is correct
• To hypothesis: some parts similar, others different

Challenges Faced

• Learning R
• Analyzing plots
• Scheduling conflicts
• Team communication

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Proposed Projects

• Genetic involvement in other disorders or disabilities
• Autism, aspergers
• Epigenetics
• How environmental factors may affect gene expression
• Sickle Cell Anemia + Malaria relationship

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One thing I learned

• R is really interesting!
• In the future, I will strive to become more fluent in R

Thank you!