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To determine which of our primary candidate genes for Fatq2b were differentially expressed, gene expression was quantified in Atp5e, Ctsz, Gnas, Rab22a and Stx16, and two housekeeping Gus and SDHA.
It considered the read counts bias by estimating the probability weighting function and used resampling strategy beyond the differentially expressed gene expression so that it can highlight GO categories more consistent with the known biology.
The top 100 ranked genes from each of the 6 analyses based on either p-values from limma (R package used to identify differentially expressed gene expression probes) or feature weights from sparse k-means or integrative sparse k-means clustering were used as input into DAVID v6.7 [ 25, 26] to identify enrichment for KEGG biological pathways.
The genes included in the VMus3D analysis were also filtered to eliminate genes that were considered to have not been expressed (gene expression levels less than 50, or log2base of ~5.64, in either mean myoblast or myotube) from the C2C12 differentiation dataset.
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We introduced a term called virtual chromosome (VC) which evaluates the prognostic score (observes significant differentially expressed gene expressions between two prognosis groups) of each gene in order to extract the prognosis based gene signature.
Different sex differentially expressed genes expression level in different organs are different.
In order to identify differentially expressed genes, Expression Logratios were analyzed using Genespring v7.0 software (Agilent Technologies).
In order to verify this hypothesis, we compared the tissue specificity between the ubiquitously expressed genes (expression breadth ≥ 14) and the intermediately expressed genes (expression breadth = 8 or 9) with similar expression level.
Of the 292 ubiquitously expressed genes (expression breadth ≥ 15), 232 contained CpG islands, and 30 genes had CpG islands that did not overlap with a TSS.
Expressed genes (expression levels 2 standard deviations above the mean of the background) were noted, anti-log transformed, and used for subsequent analysis.
Of the total of 5384 genes selected by microarray analysis, the number of relatively highly expressed genes (expression ratio > 0.1) accounted for approximately 7%, whereas it accounted for 20% of the 618 genes of the poly(A) data set.
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