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Many transcripts clustered into families of related genes with stage-specific expression.
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In many transcript clusters such as 2899110 (HFE, a gene important in iron metabolism) shown in Figure 4A, probe selection increased the absolute values of gene expression indexes (green rectangles vs red triangles) in each sample.
Many transcripts within Cluster 4 (69/86) were found to be down-regulated in our mock transfection experiments during immune stimulation by Lipofectamine and RISC-Free siRNA.
Underexpression of many transcripts found in cluster B has been previously reported in several models of aging and AD as well as in AD patients.
Even though this cluster contains many transcripts, it represents <10% of the total number of transcripts.
These three clusters included many transcripts homologous to the well-established phosphate-starvation induced (PSI) genes coding for e.g. purple acid phosphatases (PAPs), phosphate transporters (PHTs) or SPX proteins, with expression of these genes under –P highest in the MCR.
Enriched in GI-cluster 5 were many transcripts (representing 251 unique gene IDs) that were expressed specifically in the small intestine and encode the machinery for the digestion and absorption of nutrients.
NOVA crosslinks to many transcripts in both nuclear/intronic and cytoplasmic/3′ UTR clusters, suggesting an ordered set of cis-actions on target RNAs.
Cluster TE Down includes many transcripts involved in the translational machinery itself, particularly ribosomal structural proteins of which the most significant pathway affected involved eIF2 signaling (p=2.35 × 10−17) (Table 1).
Hit clusters and oligoadenylated fragments were recovered at multiple sites on many transcripts, suggesting that repeated rounds of surveillance factor binding and oligo(A) addition may be needed for complete substrate degradation.
When examining the other two cluster groups (indicated by IV and V on Figure 5), many transcripts were identified that have already been reported to have roles in processes that occur during early meiosis.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com