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Volcano plots displaying differential expression. The y axis corresponds to the negative false discovery rate on a log10 scale. The x axis displays the M value (log2 fold change). Differential expression (proportion of false positives < 0.025): (a) between TNF-positive patients and nonresponders (685 differentially expressed (DE) genes) before treatment, (b) before and after treatment in the good responders (115 DE genes), (c) before and after treatment in the moderate responders (0 DE genes), (d) due to treatment in the nonresponders (no DE genes), (e) before and after treatment in all patients (974 DE genes), and (f) before and after treatment in the TNF-positive group of patients (1058 DE genes). TNF-α is highlighted in (e) and (f). FDR, false discovery rate.
Interestingly, the highest number of DE genes (685) was found in
the comparison of TNF-positive patients and nonresponders (Figure
The results are presented in Figure 2b–f.
In the good responders 115 genes were DE (Figure 2b), whereas no
genes reached significance in the moderate responders or the
nonresponding patients (Figure 2c,d).
A total of 974 genes were DE (Figure 2e) when testing for the
effect of treatment using all patients, but the largest effect
(1,058 DE genes) was observed in the TNF-positive group of patients
(Figure 2f, Additional file 8)..
Analysis of differentially expressed genes before and after
treatment in all patients simultaneously resulted almost as many
significant genes were detected (974 DE genes) as in the
TNF-positive group, but as exemplified by TNF-α in figures 2e and
2f important observations can be missed if confounding cohorts used
to test for a specific effect with unaffected/moderately effected
Lindberg, Johan; af Klint, Erik; Catrina, Anca Irinel; Nilsson, Peter; Klareskog, Lars; Ulfgren, Ann-Kristin; Lundeberg, JoakimJournal: Arthritis Research & Therapy
Issue 6DOI: 10.1186/ar2090Published: 2006-12-01Institution(s):
School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Karolinska Institute, Karolinska University Hospital
This image is from the article titled "Effect of infliximab on mRNA expression profiles in synovial tissue of rheumatoid arthritis patients"
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