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Using the attained Entrez Gene IDs as identifiers of genes, we obtained the total lists of both Gene Ontology terms and KEGG pathway descriptors, with which our selected set of genes was annotated and analyzed using the DAVID functional annotation tool [14] with the most recent data update (January, 2008).
When the method was tested in rice starting from a group of co-expressing Late Embryogenesis Abundant (LEA) genes, we obtained a promoter similarity-based network that contained candidate genes that could plausibly complement the function of LEA genes.
For some phase (opa, pilC) and antigenic (pilin) variable genes, we obtained various sequences in the blood isolate.
To test the remaining 8 potential RhoGEF genes, we obtained deficiencies predicted to uncover these genes from the Bloomington Drosophila stock center.
Second, using the Gene Ontology database to identify cell adhesion-related genes, we obtained 1719 individual probe sets corresponding to genes involved directly or indirectly in cell adhesion.
Because a miR can regulate multiple genes, we obtained a list of 205 genes in Targetscan 5.1 (http://www.targetscan.org) that are putatively targeted by miR-212, and examined their gene expression levels in SCC1 and 1Cc8.
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Our research team has shown that by simply silencing one of those 'susceptibility' genes, we obtain a Chardonnay clone resistant to powdery mildew.
That is, for some genes we obtain orderings which are worse than lists picked by random.
Excluding these genes, we obtain our final catalogue of 893 putative synaptic genes.
Focusing on these genes, we obtain 2,397 associations between 1,572 diseases and 1,391 genes.
In the validation against random genes, we obtain an MRR of 10.19% and an AUC of 90.72%.
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