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Additional file 9: Table S1. of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

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posted on 26.04.2016, 05:00 by Enoch Antwi, Jurgen Haanstra, Gowthaman Ramasamy, Bryan Jensen, Dorothea Droll, Federico Rojas, Igor Minia, Monica Terrao, Clémentine Mercé, Keith Matthews, Peter Myler, Marilyn Parsons, Christine Clayton
Datasets used for modelling, with results. Data are taken from [16]. Sheet 1: We chose coding regions for which there had been no more than 2-fold differences in either copy number, or mRNA abundances, between 2 different experiments in bloodstream forms. The error in the half-life measurement in bloodstream forms (residual sum of squares) was also less than 0.3. Sim = simulated results; results for model BS-D (columns L & M) were used for the main analyses but those for BS-A and BS-E are also included in columns R-U. Column P has the following categories: “1. High”: mRNA amount is at least 4 times higher than expected; “2. Low”: mRNA amount is at least 4 times less than expected; 3. Normal: mRNA amount is less than 4 times more or less than expected. Column Q is like column P except that the boundary is within 2-fold. Sheet 2: As for sheet 1, but for procyclic forms. In this case mRNAs were taken for which the standard deviation of 3 abundance measurements was less than twice the mean. Sim = simulated results; results for model parameters PC-A (columns L & M) were used for the main analyses but those for PC-B are also included in columns R&S. Sheet 3: Coding regions from sheet 1 for which there was a measured bloodstream-form splicing time of less than 5 min; used for testing all bloodstream-form models except BS-C. Sheet 4: Coding regions from Sheet 4 for which the next gene downstream also had a measured splicing time of less than 5 min; used for testing bloodstream-form model BS-C. (XLSX 1679 kb)

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