PDAC miRNA clinical project

This repository demonstrates an independent analysis of miRNA differential expression in Pancreatic Ductal Adenocarcinoma (PDAC), using publicly available datasets.

Data

• Source : Gene Expression Omnibus (GEO), accession GSE226762 .
• Raw miRNA count matrices and Patient information data are available under data1/.

Workflow

• Preprocessed data and normalization . (processed/results)
• Differential expression analysis and visualization via R . (scripts/mirna_analysis.R). (results/)
• Output: DE miRNA table : (results/DE-miRs from PDAC Patient Tissue.csv/) and volcano plot :( results/DE-miRs of PDAC patient.jpeg )

Objective : To Find Differential expression analysis of microRNAs (miRNAs) in pancreatic ductal adenocarcinoma (PDAC) using publicly available datasets.

Data type : miRNA expression counts (tissue samples).

• Process:

  • Selected tissue-specific samples.

  • Cleaned sample IDs to match metadata.

  • Saved processed count matrix in processed/.

    Methods

  • Data Cleaning

  • Filtered sample data and matched with metadata

  • Prepared expression count matrix

  • Differential Expression Analysis

  • Performed with DESeq2

  • Threshold: log2 fold change ±1, adjusted p-value < 0.05

  • Visualization

  • Volcano plot using ggplot2

  • Highlighted significantly up/downregulated miRNAs

    Result

    • DE-miRNA table: results/DE-miRs from PDAC Patient Tissue.csv/
    • Volcano plot: results/DE-miRs of PDAC patient.jpeg