Augmented Gene Set Enrichment Analysis (AGSEA) Appyter скачать в хорошем качестве

Augmented Gene Set Enrichment Analysis (AGSEA) Appyter

Gene set enrichment analysis, GSEA, is an analytical method used to interpret gene expression data. Although there are variations, the standard method consists of calculating an enrichment score, estimating its significance, and then adjusting for multiple hypothesis testing. The AGSEA Appyter is a web application that performs this standard method, as well as an augmented feature, when provided with a set of inputs. For submitting expression data, the user can either choose to supply a pre-ranked list of genes, or an expression dataset with counts and a phenotype labels file along with a ranking method. The user must also submit a gene set library, which can be a chosen Enrichr library or uploaded by the user themselves. Finally, the user has the choice of specifying the number of top gene sets that the appyter will display, what criteria they will be sorted by, and whether they would like the appyter to highlight co-expressed genes. From these inputs, the appyter performs the GSEA method and displays a table with the enrichment result statistics for the top gene sets, with the full results available to download. There are also interactive Hit Indices and Enrichment Plots generated for these top gene sets. If an Enrichr library is chosen and the user wants to highlight co-expressed genes, the appyter will also analyze an augmented version of the gene set library and supply the top co-expressed genes from the results of random walks. In conclusion, the AGSEA Appyter is a useful tool for biologists to interact with visualizations of GSEA results and gain insight into their data. This presentation is by Cindy Xiong, an undergraduate student at Carnegie Mellon University. Cindy describes her summer research project with the BD2K-LINCS DCIC in the Ma'ayan Lab at the Icahn School of Medicine at Mount Sinai. https://appyters.maayanlab.cloud/#/GS... https://labs.icahn.mssm.edu/maayanlab/