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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.
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CellQuest software was used for analyses of the list mode data (LMD).
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.
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.
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).
Additional file 5: Table S5 displays GeneCodis functional analyses of the genes listed in Additional file 4: Table S4.
Moreover, analyses of this list of prospective tetramers allow the retrodiction of several experimental results, thus demonstrating its predictive value.
In house scripts written in Perl were used for the downstream analyses of the obtained SNP lists as well as for making the coverage plots.
Functional analyses of the resulting gene lists were performed using DAVID version 6.7 [ 67, 68].
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