This allowed for the calculation of a "variable fold-change" threshold for any absolute intensity at any level of statistical confidence. Testing of this method indicates that it removes intensity-specific bias
test, which is based on the analysis of the distribution of intensities of all features on a microarray mapped to a three dimensional feature space composed of the average difference of gene expression (logarithm of fold change), total variance and average expression level. it introduces a score...
Disruption of the stem loop by non- compensatory mutations is known to change gene expression7. To explore a possible regulation by RNA-binding proteins, we determined binding partners to this structure and applied our quantitative proteomics workflow comparing the wild-type PMA1 hairpin to a ...
fold change (DFC) test, which is based on the analysis of the distribution of intensities of all fea- tures on a microarray mapped to a three dimensional feature space composed of the average difference of gene expression (logarithm of fold change), total variance and average expression level....
We use total counts for the normalization of raw counts, to rectify the batch sequencing deptch. Because some sgRNAs in the reference have very low raw counts, which can affect the fold change calculation of the following analysis. We define sgRNAs counts less than 0.05 quantile both in refe...
Gene-wise statistical analyses of gene expression data, for which the significance relative to a fold change threshold is important, give reproducible and reliable results on NanoString data of mouse odorant receptor genes. Because it can be difficult to set in advance a fold change threshold that...
r̄i value associated to gene i. Thus, we use a trimmed mean by removing a percentage of low and large ranks in the calculation of r̄i. This percentage is a tuning parameter of the FCROS method which is summarized as follows (see also Figure 1). Figure 1 Steps of the FCROS ...
(Fig.1b). Disruption of the stem loop by non-compensatory mutations is known to change gene expression7. To explore a possible regulation by RNA-binding proteins, we determined binding partners to this structure and applied our quantitative proteomics workflow comparing the wild-typePMA1hairpin to...
Disruption of the stem loop by non- compensatory mutations is known to change gene expression7. To explore a possible regulation by RNA-binding proteins, we determined binding partners to this structure and applied our quantitative proteomics workflow comparing the wild-type PMA1 hairpin to a ...
based on the calculation of the change in solvent accessible surface area for fully folded monomers, the expected upper limit of the summedmvalues is 67%. This comparison suggests that the partially folded monomers are overly collapsed relative to the extended structure seen in the handshake motif...