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In order to judge the extend of functional co-occurrence that is expected by random chance we randomize gene labels for each network and compute d r from 100 randomizations.
By random chance, we expect 5% of the tissues to show significance at p-value threshold of 0.05.
To compare how significant the enrichment score of a top ranked term from SLEPR result is on the DM2 dataset to that of a gene set by random chance, we generated 2000 randomly selected gene sets of the same size as the gene set "Oxidative Phosphorylation (MOOTHA_VOXPHOS)" (80 genes per gene set) from annotated genes in the GSEA database or MSigDB.
To determine the expected percentage of two drugs sharing at least one common target by random chance, we generated 10,000 random drug pairs, and assessed how many of them target at least one common molecule according to the DrugBank drug-target information.
To assess whether 'energy' related transcripts were significantly overrepresented in the identified sense-antisense transcript pairs than was expected by random chance, we performed a hypergeometric test.
To make sure that the negative correlations were not obtained by random chance, we compared these fractions with the corresponding fractions in random sets of expressed miRNAs and mRNAs of the same sizes as the identified MTBs.
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To test the specificity of our pathway analysis and if the common pathways could be identified by a random chance, we created 10 sets of 300 randomly selected genes (not differentially expressed).
As the observed downregulation is much more than expected by random chance and we observed significant downregulation in multiple cancers, this finding is unlikely to be a false positive.
However, as each of our tissue samples typically gave only 35 50 TRFLP peaks from an empirically determined pool size of 314 peaks, the sharing of so many 16S restriction polymorphisms from different tissue samples could not have occurred by random chance, which we demonstrated statistically (Additional file 6: Table S3).
By random chance (estimated by reshuffling the gender) we would expect a ratio of 4.94 for those people.
FDR allows for the comparison of significant sites in our candidate genes to those we would expect to see by random chance alone.
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