PECAplus: statistical analysis of time-dependent regulatory changes in dynamic single-omics and dual-omics experiments

a Schematic diagram of PECAplus modules. The pre-processing module performs data smoothing and missing data imputation. The processed data goes through a mass action modeling module of user’s choice, and post-processing GSA module is applied to summarize time-dependent regulation patterns for biological functions. b PECA core analysis input and output in SLC39A14 gene. The four panels show the RNA and protein expression data, with solid dots and clear circles representing observed and GP-smoothed data points, respectively. Red circle and blue solid circle are imputed protein expression value at 16？h by GP and k-nearest neighbor imputation method. Fitted trajectory is the consensus time course profile across the two replicates reported from the PECA model. c The panels on the right side show the inferred rate ratios and CPS values for RNA-level and protein-level regulation. Red dashed lines are the CPS thresholds at 5% FDR (0.83 for RNA, 0.88 for protein