Journal Entry: Assignment 3 - bcb420-2022/Emiliya_Stolyarova GitHub Wiki

Started: March 26, 2022. Completed: April 6, 2022.

A3_EmiliyaStolyarova.Rmd
A3_EmiliyaStolyarova.html

Progress

GSEA

For the GSEA homework completed previously, I downloaded the GSEA GUI (Mootha et al., 2003; Subramanian et al., 2005). For this assignment, I was able to figure out how to open the docker image including GSEA, version 4.1.0, which I will be using. At first, I had trouble creating the command which would perform the GSEA preranked analysis. Most of my errors came from the format of my ranked gene list file. I had to Remove the genes which had a blank hgnc symbol and which had a NA gene symbol. I also had to change the file format from .txt to .rnk. In the end, I was able to complete this GSEA analysis on my ranked gene list using the docker image.

Cytoscape

For the data I am using (Huangyang et al., 2020), at an FDR threshold value of 0.01 or less, only genesets for negatively regulated genes are displayed. Therefore FBP2, which has been experimentally upregulated, is not found in the enrichment map. The FDR threshold has been increased to 0.05, which introduced two red nodes of upregulated genes, but they do not contain FBP2. This most likely indicates that the downregulation of genes caused by FBP2 is more significant that the experimental induced expression of FBP2 in the cells.
The Node table and the edge table have been downloaded as csv files to see how many nodes and edges there are in the enrichment map.
When collapsing the annotated enrichment map, it is important to change the preferences to "Enable attribute aggregation’’. If this preference is not changed, there will be grey nodes. I had to change this preference in order to achieve the collapsed theme network. The legends for the networks, which are found through the EnrichmentMap app (Merico et al., 2010), had to be manually put onto the generated PNG images through a photoediting application.

Dark Matter

Interestingly, gene ranks can equally be used to determine whether a gene has significant expression since they are derived from the p value. If the significance threshold of the p value was 0.05, the expression -log(0.05) can be used to determine the significance of the ranks of genes. The heatmaps in Assignment 3 were created with the same methodology as the heatmap of the entire expression data in Assignment 2.

References

Huangyang, P., Li, F., Lee, P., Nissim, I., Weljie, A. M., Mancuso, A., Li, B., Keith, B., Yoon, S. S., & Simon, M. C. (2020). Fructose-1,6-bisphosphatase 2 inhibits sarcoma progression by restraining mitochondrial biogenesis. Cell Metabolism, 31(1), 174–188.e7. https://doi.org/https://doi.org/10.1016/j.cmet.2019.10.012

Merico, D., Isserlin, R., Stueker, O., Emili, A., & Bader, G. D. (2010). Enrichment map: A network-based method for gene-set enrichment visualization and interpretation. PloS One, 5(11), e13984.

Mootha, V. K., Lindgren, C. M., Eriksson, K.-F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstråle, M., Laurila, E., & others. (2003). PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nature Genetics, 34(3), 267–273.

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498–2504.

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., & Mesirov, J. P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545–15550. https://doi.org/10.1073/pnas.0506580102