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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Analyzing magnetic bead QuantiGene® Plex 2.0 gene expression data in high throughput mode using QGprofiler

Fig. 2

Overall QGprofiler quality assessment and data (pre-)processing analysis flow represented by the different hexagons and illustrated by different QGprofiler’s screenshots. a QGprofiler interface, with required user-supplied inputs on the left panel and output on the right panel. Output is organized in three: general plate information (Plate tab, shown); various quality control steps (QC tab); and dose response modelling results and export options (Results tab). The Documentation tab provides extensive information on QGprofiler usage. The Plate tab provides a visualization of the experimental setup of the plate as well as information on which well/genes are disregarded based on minimal number of beads or LOQ10. b Quality control of background signals. MFI counts for each background well are depicted across all measured genes. Blue, red and green lines indicate the limits of quantification, set at 3, 5 and 10SD (LOQ3, LOQ5 and LOQ10). These are calculated as the mean MFI value across all background wells plus three, five or 10 standard deviations of the background, respectively. c Quality control of background corrected signals in function of cell count for a series of HKG (more HKG were tested, data not shown). As a rule of thumb, LOQ10 can be regarded as the lower limit of HKG signal linearity. d Quality control on HKG stability on a 20% FC range, expressed per HKG, cell density, exposure time and/or cell line. e Dose response relationship of background corrected HKG MFI values, indicating cell cytotoxicity. The horizontal dashed lines indicate the background corrected MFI threshold based on the negative controls for the corresponding HKG. f FC barplot on a per-gene basis, across the different compound concentrations in which each compound dilution series is plotted with a separate gradient color. Across this specific experiment some compounds show almost no effect, while others reveal a clear dose-response relationship. g Example of the final dose response 3PL model for a gene of interest in cells exposed to a compound of interest. Dotted horizontal line represents the absolute AC50 level

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