Table 1.
Functionality of currently available motif scanning tools.
Fig 1.
Validating the mixed Student’s t-test with simulated and real-world data.
A and B. Simulated data and representative real-world data testing; the distribution of bkg was colored with gray, and obs with dark green; the one values of interest were indicated with vertical lines. C. Parameter testing. The X axis represented the coefficient of conserved variation (CCV, 0 to 2.0), the Y axis represented the standard deviation (SD, 0 to 3.0), and the Z axis represented the 1 − p-value. D. Schematic of the pipeline used for the study.
Fig 2.
Performance assessment of motif scanners in analyzing ReMap datasets.
A total of six scanners (Clover, FIMO, Grit, Pscan, PWMScan, and Swan) were evaluated based on the parameters of sensitivity (Sn), positive predictive value (PPV), geometric accuracy (ACCg), and total number of predicted transcription factor binding sites (TFBS, Count).
Table 2.
Performances of Grit with FIMO using publicly available Chip-seq datasets with literature support.
Fig 3.
Differences among the results of Grit and other prediction tools.
A. Number of transcription factor binding sites (TFBS) that overlap (light green) between Grit and other prediction tools, and Grit specific (red) or other tool specific (light blue) TFBS. B. Overall comparison of numbers of TFBS between prediction results of Grit and other prediction tools. The violin plot in C and D shown distributions of conserved variation (CCV) and standard difference (SD) for TFBS identified by Grit but did not by other tools (Grit–other, the symbol “–” means subtracting), respectively.