Please note that in this video, Saniya goes through how you can use g:Profiler ([ Ссылка ]) to perform gene-set enrichment analysis (GSEA), along with other functions, and also download gene data sources as .gmt files. That is, for a given list of genes (gene names and/or gene Entrez IDs or Ensembl IDs), you can use g:Profiler to uncover biological pathways, networks, functions, associations, tissues, etc. that are enriched (have a statistically significant overlap with our gene list) for our list of genes. In short, through Metascape (1 of many tools out there), we can query hundreds of different biological gene lists (across a variety of databases and atlases like Gene Ontology, biological pathways (e.g. KEGG, Reactome, WikiPathways), regulatory motifs in DNA (e.g. TRANSFAC, miRTarBase), protein databases (like Human Protein Atlas or CORUM), human phenotype ontology (e.g. HP) to determine what significant biological results are there for our gene list. Saniya also explains how results differ for different gene sets.
Please reach out if you have any questions or comments and please subscribe to Saniya Khullar's channel for more updates. Thank you so much!! :)
Also, if you would like to "buy me a cup of coffee" as a thanks, I would really appreciate it (even more so especially as I am still a student living on a stipend): [ Ссылка ]
Please note other gProfiler videos by Saniya:
* g:SNPense (variant impact) for SNP rsIDs (mapping to protein-coding genes): [ Ссылка ]
* gProfiler GOSt is used to perform functional enrichment analysis, also known as over-representation analysis (ORA) or gene set enrichment analysis, on an input gene list. Video: [ Ссылка ]
* gProfiler Convert helps convert between various gene, protein, microarray probe and various other namespaces: how do you convert gene ids of 1 type (e.g. Entrez gene ID) to those of another type (e.g Ensembl gene IDs)? Video: [ Ссылка ]
* gProfiler Orth translates gene identifiers between organisms: how do genes in 1 organism map to genes in other organisms? Video: [ Ссылка ]
* gProfiler overview of the tools: [ Ссылка ]
Saniya also has a video on another tool: Metascape for Gene Set Enrichment Analysis: [ Ссылка ]
