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The Cancer Genome Anatomy Project (CGAP) was designed and implemented to provide public datasets, material resources and informatics tools to serve as a platform to support the elucidation of the molecular signatures of cancer.
Stat5a and Stat5b mRNA expression levels were evaluated in the context of clinical outcome in RNA microarray datasets (Material II) compiled from public repositories, Gene Expression Omnibus [ 36] and ArrayExpress [ 37], as described previously [ 38].
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We used periods with overlapping information (1876 1900, 1901 1925 and 1926 1950; N = 98 species/groups of species) for the intercalibration between the two datasets (Materials and Methods S1).
Supplementary dataset, materials and methods, figures S1– S5, and tables are available at Genome Biology and Evolution online (http://www.gbe.oxfordjournals.org/).org/
We mined these large datasets for material responses by employing matrix decomposition techniques, such as independent component analysis.
To address each of these questions we used three different datasets (see Material & Methods for a detailed description).
In total, 4363 SNPs within these 77 candidate genes were investigated in the two GWAS datasets (Supplementary Material, Table S2).
Each protein domain sequence in our dataset has <40% sequence identity to any other sequences in the training, testing and benchmarking datasets (Supplementary Material 1 and 2).
For further details, the assembled genome, and the list of genes used in this study see the supplementary section Resources and Datasets (Supplementary Material online).
We found that EPCAM was not differentially expressed between uninflamed and inflamed tissue in both the CD and UC datasets (supplementary material Fig. S5A,B).
For further details and the list of all genomic features used, see the supplementary section Resources and Datasets (Supplementary Material online).
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