Yeast SAFE Analysis
Description
SAFE (Spatial Analysis of Functional Enrichment), is a systematic methodology for biological network annotation and their functional organization. The SAFE method relies on three major steps: first, attain a network map containing all of its nodes and connections; second, collect multiple independent datasets that characterize all nodes relative to one another based on parameters such as cellular localization, mutant phenotype, transcriptional response; and third, perform automated statistics to identify regions with functional relevance through the overlay of functional data and the network map . For target pathway identification by HOP, we extracted the top the top 10 genes involved in both positive and negative genetic interactions for each single-deletion mutant hit. The lists of genetic interactions were generated through a yeast global genetic interaction network platform (thecellmap.com), by the selection of the top 10 genetic interactions with a P value < 0.005. Final lists were then analyzed in the same platform by Spacial Analysis of Function Enrichement (SAFE), to find regions of the global similarity network that are significantly enriched for genes that interact with HOP hits, using a stringent cutoff for both genetic interactions. The files contain the SAFE analysis provided by the genetic interaction network platform (thecellmap.com), used to predict the targeted pathways affected by 0CK and 542 compounds.
Files
Steps to reproduce
For target pathway identification by HOP, we extracted the top the top 10 genes involved in both positive and negative genetic interactions for each single-deletion mutant hit. The lists of genetic interactions were generated through a yeast global genetic interaction network platform (thecellmap.com), by the selection of the top 10 genetic interactions with a P value < 0.005. Final lists were then analyzed in the same platform by Spacial Analysis of Function Enrichement (SAFE), to find regions of the global similarity network that are significantly enriched for genes that interact with HOP hits, using a stringent cutoff for both genetic interactions.