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DOI: http://dx.doi.org/10.7554/eLife.00522.026 10.7554/eLiFigure22.027 figure 7—figure supplement 1. Supplementary misexpression predictions of the eve 2 and eve 3+7 linear (A,B) and quadratic (C E) models.
For the on-line supplementary data, predictions were derived from either using all attributes or subsets of the data for assessing redundancy in specific biological contexts.
We obtained a reference gene set that contained 22,168 coding genes in the BMR genome by combining homologous searching, transcriptome evidence and de novo prediction (Supplementary Note 3; Supplementary Tables 9 and 10).
The qRT-PCR products obtained were consistent with our prediction (Supplementary Figure S4).
Among all of the HrpL up-regulated genes identified in the microarray study (Table 1) and HMM bioinformatics prediction (Supplementary Table S3), dspA/E is the only gene confirmed to encode a potential T3SS effector in 3937 [24].
A debriefing questionnaire confirmed this prediction (Supplementary material).
A relatively wide range of PT values was obtained in the population prediction (Supplementary Figure S2a,b).
As expected (and as in the case of the simulated data), the linear model was not well behaved for prediction (Supplementary Fig. S12) and is not shown.
We reanalysed seven RNA-sequencing data sets (total of 18 samples, including four tissues: seedling, leaf, flower and root) for transcriptome reconstruction and lncRNA prediction (Supplementary Table S1).
Proteins were classified as "uncharacterized" based on absence of literature but also had low GO coverage and weak domain-based prediction (Supplementary Fig S4).
Broadly speaking, the NRI index also suggested that the addition of the GRS risk groups did not substantially improve risk prediction (Supplementary Table 1).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com