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CellQuest software was used for analyses of the list mode data (LMD).
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Then, we performed GO/KEGG/UniProt enrichment analyses of the lists of up- and down-regulated genes, using a Benjamini cut-off of P < 0.05.
In order to analyze potential functional trends in our microarray data, we performed functional analyses of the lists of differentially expressed up and downregulated genes.
In addition to the APOE ε4 haplotype (MIM 107741), we limited out analyses to the list of SNPs that showed a genome-wide association with AD in previous literature and were replicated in additional publications.
Moreover, analyses of this list of prospective tetramers allow the retrodiction of several experimental results, thus demonstrating its predictive value.
Factor analyses of the 27 listed resistance responses suggested five clusters of items comprising internally consistent though inter-correlated subscales (Inform others, Aggression, Verbal or nonverbal refusal, Deflection, Deception).
The resulting tryptic fragments were analyzed by peptide mass fingerprint by MALDI-TOF-MS with MASCOT and PROWL analyses of the peak lists.
To test this hypothesis, we performed separate functional enrichment analyses of the two lists using the ToppGene Suite.
Additional file 5: Table S5 displays GeneCodis functional analyses of the genes listed in Additional file 4: Table S4.
The same computation was used for gene ontology analyses of the initial gene list.
We performed Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and gene ontology (GO) analyses using the list of 4648 Class A BOPs differentially methylated between DS and DSS (Table 1).
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