from 1106 transcripts in M turquoise to 35 transcripts in M darkgrey (Fig 1A). Next, to assess the quality of sample matching and to detect any confounded modules, the module eigengenes (MEs), which represent the sum of gene expression profiles of each module, were correlated to four matching demographics (age, pH, Postmortem Interval (PMI) and RNA integrity Number (RIN)) and to smoking status. Four modules were significantly correlated (adj. p≤ 0.05) with brain pH and PMI, and were removed from all subsequent analyses. Of the remaining 20 modules, six were significantly correlated with AD case-status (Fig 2A). M turquoise and M yellow were downregulated in AD cases, while M grey60, M pink, M green and M salmon were upregulated, and these six modules contained 45% of the 4571 transcripts. A full table containing module size, correlations and p-values for all mRNA modules is provided in S2 Table.
