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P-values <0.5 or >2 indicated differentially expressed genes.
Statistical analyses were performed by unpaired Student t-test for all results of in vivo studies and by one-way analysis of variance (with Bonferoni post-test analysis) for all in vitro data (unless indicated differentially) to determine statistical significance between the groups.
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Bold numbers indicate differentially expressed genes in plants subjected to each treatment.
Arrows indicate differentially expressed TDFs.
The smallest rank sums indicate differentially expressed genes are consistent among the three methods.
Global observation of the heat map indicates differentially regulated transcriptome signatures in response to non-freezing cold treatment in ten different A. thaliana ecotypes.
Around gene positions 0.12 and 0.15, upside down peaks crossing the black horizontal line at P = 0.01 indicate differentially expressed gene sets linked to RNA processing and Spliceosome while at positions 0.33 and 0.35 the upside down peaks are related to transcription regulation.
Differentially expressed genes (FC >2.0, p-value <0.05) detected by DEGseq were mapped to this hematological gene set, which indicated the differentially expressed hematological genes in our data set.
Further Gene Ontology analysis indicated that differentially expressed genes were associated with immune and inflammatory responses, leukocyte adhesion, cell migration, and signal transduction.
Results indicated that differentially expressed mitochondrial proteins were involved in the electron transport chain, tricarboxylic acid cycle, stress response and carbon metabolism.
Lowering the scores, but still in a very conservative limit, some gene sets are indicated as differentially expressed with P < 0.01 and FDR < 0.06.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com