No differences in gene complement were noted in microarray data comparison of N. gonorrhoeae strains FA1090 and F62.
Figure 1, panels A through C, shows microarray data comparison for expression of genes Tsc22, Col3a1 and Fubp1 in 2 strains assayed each in 6 microarray replicates.
While useful for microarray data comparison, MADMuscle is not limited to microarray results, and is equally capable of comparing results from other high-throughput technologies (SAGE, ChIP-on-chip or ChIP-seq, Protein-array and other proteomic analyses, large scale Real-time PCR, etc).
Statistical analyses of microarray data, mean comparisons (ANOVA F-test) and distribution comparisons (Likelihood ratio test) were performed using JMP software.
For the microarray data, multiple comparisons were performed for individual groups so the level of statistical stringency is critical, though confirmation by qRT-PCR partially mediates this concern.
The results from three conditions (E2, GFs, and cAMP) are shown in Figure 2 along with a dendrogram representing the microarray data for comparison.
From the microarray data, a comparison of lncRNA expression levels between PDLSCs and BMSCs identified an average of 970 lncRNAs that were significantly differentially expressed (see Supplementary Table 1 in Supplementary Material available online at http://dx.doi.org/10.1155/2014/317853); of those, 457 were upregulated and 513 were downregulated in the PDLSCs compared to the BMSCs.
(a) The expression levels of ECM-related genes is upregulated across models (marked in bold in A, C) in a separate microarray data set in comparisons between albumin vs. albumin + TGFβ receptor (R) blockers.
Additional microarray data manipulations and comparisons were assessed using Microsoft® Excel and Microsoft Access 2002 (Microsoft, Redmond, Washington, USA).
