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Based on these gene programs, biological processes and cellular pathways overrepresented in developing cells at each particular time point could be deduced.
Thus we rely only on the gene sets on which the gene signatures are based, and fit survival models based on these gene sets without depending on the quantitative specifics of the published gene signatures.
Based on these gene sets, we asked whether the core DAF-16 regulon and the species-specific DAF-16 regulons differ in the type of genes they contain by testing whether particular gene ontology (GO) terms (using GOTERM BP_ALL and GOTERM BP_2) are overrepresented (Table S6 and Table S7).
Nevertheless, based on these gene expression levels we cannot assess the pluripotent state of the analyzed cell lines.
The corresponding analysis comprises inferring differentially expressed genes and, based on these gene wise probabilities, inferring GO term activity.
For multi-sample comparison, microarrays based on these gene collections can detect changes in gene expression and species interactions at the gene level [ 26].
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Then molecular signatures are developed based on these genes using a nearest-centroid prediction method [47].
A concatenated sequence based on these genes was used for a phylogenic analysis with homologous loci of other TBRF Borrelia species.
One hundred and thirteen genes were identified as significantly up-regulated in patients with sporadic TAA (average FC>1.3 and FDR<4%) and hierarchical clustering based on these genes clustered the familial and sporadic TAA patients into distinct branches (Figure 5B) (Table S3).
All subsequent selections and analyses were based on these genes referred to as REGγ correlated genes.
However, cluster analysis based on these genes could not reproduce the unsupervised clustering.
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