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For quantification of overlap of peaks in bivalent promoters, we wrote custom software.
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In summary, this quantification of overlapping thalamic territories shows, for the projections to cortical areas of different modality, a territory of overlap mostly at the level of the posterior thalamus (Fig. 4 D – I ).
Whereas it is relatively easy to find identical compounds in two datasets, the quantification of the overlap is not straightforward.
(D ) Quantification of the overlap between GluA1 and Arf6.
A. Quantification of the overlap between GluA1 and Arf6.
(F ) Quantification of the overlap (Pearson's correlation coefficients, Rr) between TC10 and Arf6 in (C ).
We have added a quantification of the overlap between an ER marker calreticulin and Mit-TEER in the text (Results, last paragraph).
For the quantification of marker overlap, single-positive cells for each marker and double-positive cells were counted in cross-sections of seminiferous cords (juvenile) or seminiferous tubules (adult).
Bar: 10 μM (C ) Quantification of SEC31A overlapped with ERGIC53 shown in (B ) using the Pearson's correlation coefficient (PCC).
(B ) Quantification of the apparent overlap in VGlut1/VGlut2 puncta, which is decreased between P15 and P25 in the WT.
One unsatisfactory aspect of the statistical analysis presented in this paper is the over-reliance of test of significance as opposed to quantification of the degree of overlap by appropriate indexes such as odds ratio or enrichment fold-changes.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com