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For details of the datasets refer to the Supplementary Table 1 in Additional file 2. We first identify gene pairs which consistently demonstrate higher correlation in cancer versus non-cancer datasets based on a robust correlation estimator, the normalized Percentage Bend correlation (for details see Methods).
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Gene expression data used in this study were publicly available and ethical approvals have been obtained as reported in the original publications to which the datasets referred.
The first row in the table shows the names of the datasets referred throughout the manuscript, and each column contains the list of genes, referred to by their official gene symbol.
Due to their different origins, the datasets referring to mature mycorrhizal roots (ARB, CMR, EPI) or early infection events (APP, NAP) were analyzed separately both for detectable expression in single cell-types and for expression differences between them.
In order to ensure that all protein-protein interactions in the dataset refer to direct contact between proteins, protein interactions within the same complex but without direct contact were excluded.
This procedure resulted in the dataset, referred as PDBTM, containing 641 whole helices involved in contacts.
Each point in the dataset refers to some measure of malaria prevalence in a given health facility (h) during a given week.
The regression line is shown in Figure 2. To evaluate the performance of gene prediction methods, we used the dataset referred to as Set 1 by Korf et al. [ 12].
For more details about the SW and DTM datasets, or to access these datasets, refer to Crossa et al. (2010).
The task was temporally structured into four periods, associated with the release of the CHEMDNER corpus datasets (refer to [21] for a detailed description of the corpus).
In the following, the same algorithm is tested on different datasets (refer to Section 2.2).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com