This repository contains the results and documentation for a bioinformatics project focused on the discovery of new molecular biomarkers and potential drug targets for Alzheimer's disease (AD). This work was conducted by interdisciplinary teams as part of HIDS-7003_2023 Midterm Project.

As part of an interdisciplinary team embedded into a neuro-biology lab, this project involves analyzing gene expression data from human brain tissue samples at various stages of Alzheimer's disease, ranging from normal controls to severely affected subjects.

• Team 1: Joan, Gazie, Aditya, Aizhan
• Team 2: Han-shen, Prachi, Shania, Subha
• Team 3: Yukhta, Youngmin, Frankie, Sydney

Each team member independently conducted parts of the analysis and then collaborated to verify and validate results.

• Each team performed a differential gene expression analysis comparing different stages of AD with normal controls using R.
• Outputs:
  • Aizhan_incipient_control_TTest.csv
  • Aizhan_incipient_control_DEGs.csv

• Analysis of DEGs using enrichR for pathway and gene ontology enrichment to interpret biological implications.
• Outputs:
  • Aizhan_incipient_control_EnrichR.xlsx
  • Aizhan_incipient_control_ShortListedPathways.txt
  • Aizhan_incipient_control_ShortListedGenes.txt

• Comparison across all teams to identify commonalities and differences in DEGs at various stages of AD.
• Utilization of Venn diagrams to find overlaps between DEG lists from different stages.

• Each team prepared a PowerPoint presentation summarizing the findings.
• Presentation files named Team1_presentation.pptx.

• Each student submitted a summary Word document detailing the analysis steps, results, and conclusions.
• R Markdown files for detailed reproducibility:
  • Aizhan_GroupCompAnalysis.Rmd and Aizhan_GroupCompAnalysis.PDF
  • Aizhan_EnrichAnalysis.Rmd and Aizhan_EnrichAnalysis.PDF
• Aizhan_MidtermSummary.docx: A concise document summarizing the project.

This repository is structured to include all files as described in the outputs section for each step of the project. It serves as a comprehensive archive of all analytical processes and results.

Review the Aizhan_MidtermSummary.docx for an overview of the project and analysis. Detailed analysis procedures and results can be accessed through the R Markdown files and their respective outputs.

This project is licensed under the MIT License - see the LICENSE file for details.

• Aizhan Uteubayeva (and team members as per the respective teams listed)

This project is an open-ended exploration into genomic data. Members are encouraged to pursue further inquiries beyond the course scope to potentially uncover new biological insights.