Using DESeq2 to discover upregulated and downregulated genes in cholangiocarcinoma single celled RNA sequencing samples

Cholangiocarcinoma is highly aggressive and very lethal, with poor patient outcome as the norm. Various mutated genes were commonly associated with Cholangiocarcinoma, the most notable ones being KRAS, TP53, IDH1/2, ARID1A, SMAD4, PBRM1, KMT2C, PIK3CA, LRP1B, BRAF, BAP1, EGFR and PREX2. In this research study we analyzed intrahepatic cholangiocarcinoma single celled RNA sequencing samples to find concordant genes and apply functional annotations to identify the gene’s functions. 5 tumour samples and 1 adjacent tissue sample were used for this research. We used DESeq2 as the main pipeline for differential expression analysis and applied data filtering to filter away non-significant SNVs and genes. The leftover SNVs and genes associated from each sample were then analyzed for concordance. We found mutations in TP53, MAPK1, MAPK3, CDH1 to be enriched in the 6 samples instead. We have also identified multiple molecular pathways up and down regulated in cholangiocarcinoma SNVs, with protein binding and RNA binding pathways being the most effected in up and down regulation of SNVs.

Author

• Chan, Kwan Hang

Language

• en

Date created

• 2023

Type of Work

• Master's Thesis

License

• All rights reserved

Rights statement

• In Copyright

GW Unit

• Bioinformatics and Molecular Biochemistry

Degree

• M.S.

Advisor

• Horvath, Anelia

Persistent URL

•  https://scholarspace.library.gwu.edu/etd/3r074v78b