Journal of Molecular Biology

Dataset (test set) of synthetic 2D Gel Electrophoresis protein spot images. The intended use of the dataset is the development of protein spot models. Dataset contains: im_Input_v1_1 – Input image, without secondary spots, with intensity scaling and added constant background im_Input_v1_2 – Input image, without secondary spots, with intensity scaling and added constant background, and added Gaussian noise im_Input_v1_3 – Input image, without secondary spots, with intensity scaling and added constant background, and added varying background distortions, but without Gaussian noise im_Input_v2_1 – Input image, with secondary spots, with intensity scaling and added constant background im_Input_v2_2 – Input image, with secondary spots, with intensity scaling and added constant background, and added Gaussian noise im_Input_v2_3 – Input image, with secondary spots, with intensity scaling and added constant background, and added varying background distortions, but without Gaussian noise im_Target_1 – Ground truth image (with intensity scaling and without background) im_Target_2 – Ground truth image (with intensity scaling and with constant background) im_Mask_1 – mask for the im_Input_v1_x input images (input images are without secondary spots so the mask covers entire image patch) im_Mask_2 – mask for the im_Input_v2_x input images (mask shows region of the primary spot)

DNA sequences (primers, gene inserts, and vectors)

Single turnover kinetic data for the cA4 degradation by the enzyme Tthb144

DNA sequences

DNA sequences

The data comprises the raw data files of the manuscript titled "Dissection of protonations sites for antibacterial recognition and transport in QacA, a multi-drug efflux transporter", authored by Majumder et al.

Table S1A. All hydrogen deuterium exchange (HDX) peptide data for experiments examining the global exchange of PI4KIIIA, TTC7B, and FAM126A. The charge state (Z), residue start, residue end number, retention time (RT) and sequence are displayed for every peptide. In the Raw Data column, the two time points (0.3s and full) are labelled, and the relative level of HDX is coloured according to the amount of deuterium incorporated, on a blue to red continuum. The data listed for the 0.3s time point are the average of three independent experiments, with SD shown next to all HDX values. In the Normalized to Full Deuteration column, the 0.3s data has been normalised to the full deuteration measurements with the exception of those data (surrounded by black lines) where the full deuteration measurement was lower than 20% deuterium incorporation. The third column denotes the corresponding peptide centroid. Table S1B. All HDX peptide data for experiments examining the complex dynamics of PI4KIIIA, TTC7B, and FAM126A. The charge state (Z), residue start, residue end number, retention time (RT) and sequence are displayed for every peptide. The two columns represent each state examined (+/- PI4KIIIA) and contain the data for five time points. The data listed are the average of three independent experiments, with SD shown next to all HDX values. Table S1C. All HDX peptide data for experiments examining the dynamics of inhibitor specificity of PI4KIIIA, TTC7B, and FAM126A. The charge state (Z), residue start, residue end number, retention time (RT) and sequence are displayed for every peptide. The three columns represent each state examined (+/- inhibitor) and contain the data for four time points. The data listed are the average of three independent experiments, with SD shown next to all HDX values.

BFDCA is a comprehensive tool of using Bayes factor for Differential Co-expression (DC) analysis. This package contains three main functions: (1) clustering condition-specific genes into functional DC subunits; (2) quantitatively characterizing the regulatory impact of genes based on their differential connectivity within DC structures; (3) providing a DC-based prediction model to predict case/control phenotypes by taking DC significant gene pairs as markers.