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As the ashh2 mutants have a clear defect in pollen production we compared ashh2 mutant microarray data with array data for spl, ems1 and ms1 mutants [23], [24].
The Chip-Chip data and wild type vs. TF mutant microarray data were downloaded from YeastRact (http://www.yeastract.com[ 20, 21]).
Using gNCA, we determined 74 TFAs from both wild type and fkh1 fkh2 deletion mutant microarray data encompassing 1529 ORFs.
Based on comparing the wild-type and TF mutant microarray data, we could tell how one TF could affect the expression of each gene.
Third, we derived significant expression change data from TF deletion mutant microarray data to identify genes regulated by each of the TFs (Fig. 1(3)).
Since nDNA replication is also extensively affected in dpb4Δ mutant microarray data, we also normalized the mtDNA copy number by comparing the mtDNA Ct of dpb4Δ with nDNA Ct of WT cells.
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Deletion strains enriched after elutriation represent small (whi) mutants, while those depleted from the small elutriated populations represent large (lge) mutants (microarray data are deposited at ArrayExpress; E-MEXP-1200 E-MEXP-1200 E-MEXP-1200
Phenotype comparison between dxr mutant and WT, RT-PCR analysis of OsPrxQ and OsPrxIIE2 in mutant, and microarray data analysis of dxr mutant/WT using Agilent 44 K array.
Cebpa mutant HSC microarray data have previously been published (Bereshchenko et al, 2009).
Thus, it will be beneficial to investigate cli186 in the context of other light and carbon signaling mutants when microarray data becomes available.
We integrate data sets including microarray profiling and sRNA deep sequencing data from miRNA biogenesis/transport mutants, microarray profiling data of mRNAs in a developmental series, and computational predictions of conserved, genomic stem-loop structures.
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