Gene regulatory networks Sample Clauses

Gene regulatory networks. The idea of regulatory networks was first proposed by Xxxxx and colleagues in 1999. They calculated the correlation coefficients for a database with simultaneous laboratory experiments (31). Later they calculated correlation coefficients for expression data and reconstructed part of the regulatory network in Saccharomyces cerevisiae (32). Gene regulatory networks are identified based on the correlation coefficient. Genes that are co- expressed show a higher correlation coefficient than would be expected based on chance. A limitation of this first approach is that it does not take protein-protein interactions and regulation of transcription factors into account that may not necessarily be visible on gene expression level. This approach also does not consider whether genes are transcription factors and are therefore capable of regulating other genes. Among other approaches (33), Xxxxx and colleagues attempted to solve this problem with an algorithm they named Passing Attributes between Networks for Data Assimilation (PANDA) (34). PANDA solves many shortcomings of the regulatory network analysis by integrating multiple data types. Therefore, PANDA can distinguish between direct and indirect interactions in a network analysis.
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