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The similarity between two lists of length r can be described using the 'correspondence at the top' (CAT r)) plot.
In cases where we assess the correlation between reported results, we used lists of length 5 through M, where M was calculated to be four times the number of TFs with scores greater than the applied threshold.
For this comparison of different sized backgrounds, we again used lists of length 5 through M. The Spearman correlation between any two backgrounds, regardless of size, was ≥0.89 for both the Z- and Fisher scores of FoxA2, whereas the correlation value for Sox2 was ≥0.90 for either score.
To generalize these results we calculated mean global and local CAT r) and Δp-CAT r) values for lists of length r=10 and 100 of all tissue samples studied considering either all genes or the genes of the strongest overexpression spot, respectively (see Additional file 1 for details).
The Spearman correlation between the top TFs, for lists of length 5 through M (where M is derived from the lenient threshold; see Materials and Methods), was ≥0.97 for both Sox2 and FoxA2 Z-scores, ≥0.93 for FoxA2 Fisher scores, and ≥0.86 for Sox2 Fisher scores.
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The Ganges-Brahmaputra, third in discharge, is 13th (or lower) in area and well down the list of length for its two main stems taken separately.
The parameter values used by a particular ant are stored in a list of length P, where P is the number of adjustable parameters of the model.
The contour line is a list of length l giving the coordinates of the points at the organism's outer boundary (Fig. 1a).
where time is discretized as a list of length n equally separated, t (k)={Δ t,2Δ t,… n Δ t}.
The results of these global and local rank comparisons confirm the trends discussed above: global FC- and WAD-lists of length r=10 – 100 agree to about 70% on the average whereas global FC/t-shrinkage and WAD/t-shrinkage lists are identical to about 50%.
Let "D" denote our ordered binary list of length N (the total number of gene transcripts).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com