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The main advantage of transcriptome sequencing over WGS is that it provides: gene expression level information, identification of expressed fusion transcripts, post-transcriptional modification including alternative splicing, single nucleotide variants (SNV) and RNA editing events [ 20].
Thereafter comes the identification of expressed genes and deriving a correct expression value for each gene.
GeneTag™ is a novel expression profiling method that allows the visualization, quantification and identification of expressed genes whether known or novel in any species, tissue or cell type, independent of knowledge of the underlying sequence.
The project, later expanded as Mouse ENCODE and modENCODE (to include invertebrate model organisms), has driven technology development and standardization for the identification of expressed RNAs and regulatory regions.
For example, identification of expressed sequence that bridges two probe sequences can be judged a success.
Until recently, oomycetes genomics focussed only on Phytophthora spp. with the completion of genome sequencing projects and large scale identification of expressed sequences [12] [17].
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For the identification of differentially expressed genes, SnTox3 was expressed in Pichia pastoris and purified from culture supernatants.
In addition, the self-contained hypothesis is a generalization from identification of differentially expressed genes to identification of differentially expressed gene sets.
Dexseq was used for analysis of differentially expressed exons, visualization and exploration for identification of differentially expressed splice variants [ 59].
Based on UniGene cluster mapping, identification of differentially expressed genes from MPSS was compared to identification of differentially expressed genes from the microarrays.
Following normalisation, analysis of variance (ANOVA) of the J-Express program package was used for identification of differentially expressed genes.
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