Author: Prashali Bansal; Johannes Madlung; Kristina Schaaf; Boris Macek; Fulvia Bono
Title: An interaction network of RNA-binding proteins involved in Drosophila oogenesis Document date: 2020_1_9
ID: 2f9nc2to_17
Snippet: All the scatter plots and the volcano plots were generated using GraphPad Prism v.7.0.0. For creating networks or subnetworks, Cytoscape v. 3.7.1 (76) was used. To integrate IP-MS data with literature, information from databases like String v. 11.0 (77) and FlyBase (78) were used. From String, only experimental data with medium confidence range was considered. Physical interaction data from FlyBase (78) were extracted for each protein individuall.....
Document: All the scatter plots and the volcano plots were generated using GraphPad Prism v.7.0.0. For creating networks or subnetworks, Cytoscape v. 3.7.1 (76) was used. To integrate IP-MS data with literature, information from databases like String v. 11.0 (77) and FlyBase (78) were used. From String, only experimental data with medium confidence range was considered. Physical interaction data from FlyBase (78) were extracted for each protein individually. Node size calculation: For dimethyl labeling data, average of the enrichment ratios of duplicates was calculated for each protein. If a protein was found to be associated with more than one bait or identified in both label-free and labeled MS data, the highest fold change value was considered, irrespective of the experiment type. In cases where several nodes were combined into one, the highest value among the respective individual components was considered. Fig. 4 was created using
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