Assignment #2 ‐ Differential Gene expression and Preliminary ORA - bcb420-2024/Anna_Lai GitHub Wiki

Differential Gene expression and Preliminary ORA

Date March 05, 2024

Notes that are not included in the final submission. For a coherent story of the data, please refer to the HTML file generated for this assignment.

Links to Assignment 1

The R file: https://github.com/bcb420-2024/Anna_Lai/blob/main/A1_AnnaLai.Rmd

The HTML filed: https://github.com/bcb420-2024/Anna_Lai/blob/main/A1_AnnaLai.html

Data annotation update

There are 9 conditions with 3 biological replicates per condition. In total 27 samples.

Differential Gene expression

The second model I was trying to use, with both the experimental condition and cell line. Yet the number of combinations is too big. There are already 9 different conditions. The error code:

Coefficients not estimable: exp_groups$sample_groupR168H.RG.Un Warning: Partial NA coefficients for 15865 probe(s)Warning: number of items to replace is not a multiple of replacement lengthWarning: Estimation of var.prior failed - set to default value

Hence, I just used the condition group as a grouping for the data for further investigation.

Threshold over-representation analysis

G:profiler used. There is a R package for it but didn't utilize it. Completed the ORA on the web platform instead.

Interpretation

Please refer to the RNotebook.

Links to Assignment 2

The R Markdown file: https://github.com/bcb420-2024/Anna_Lai/blob/main/A2_AnnaLai.Rmd

The HTML filed: https://github.com/bcb420-2024/Anna_Lai/blob/main/A2_AnnaLai.html

Citations

For the RNotebook, I used a research aid application Zotero to generate the bib file, which I highly recommend.

• Dorison A, Ghobrial I, Graham A, Peiris T et al. Kidney Organoids Generated Using an Allelic Series of NPHS2 Point Variants Reveal Distinct Intracellular Podocin Mistrafficking. J Am Soc Nephrol 2023 Jan 1;34(1):88-109. PMID: 36167728