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Applying this tool to the mouse dataset identified group-specific DNA copy number changes for each of the seven expression-defined groups (Fig. 2).
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Although the Core dataset probes are the best annotated, the rat genome is not as well annotated as the human and mouse genomes, with many of the genes in the rat Extended dataset identified based on their similarity to human or mouse genes.
This pipeline is independent on known gene annotation and can be successfully employed in human, rhesus and mouse datasets to identify new sno-lncRNAs.
In the complete mouse promoter dataset, we identified 29 significant motifs corresponding to matches to TRANSFAC matrices, 4 to JASPAR CORE matrices, 9 to JASPAR phyloFACTS, and 22 to 6mers.
The correlations were calculated per mouse dataset.
All the datasets have been named according to the study type as prefix and species as suffix (Studytype_Species), 'Hs' indicating human dataset and 'Mm' indicating mouse dataset.
The previous human dataset and a mouse dataset were used for the comparison.
The Yeast dataset includes 44 functional association networks, the Human dataset includes 8 networks, the Mouse dataset consists of 10 networks, and the Fly dataset has 38 networks.
Only one mouse sno-lncRNA was identified from the limited available mouse datasets in RPL13A region, and snoRNAs themselves in this region have been suggested to be involved in lipotoxicity in mouse.
Pathprints were calculated for each sample using the Pathprint package in R. Pathways shared by leukemic and normal stem cells that are differentially expressed in progenitor cells were identified for the human and mouse datasets.
In this dataset we identified heterogeneity within mouse models and noted a surprising amount of interrelatedness between models, despite differences in the tumor initiating oncogene.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com