Characteristics of the 227 women in the study population^a.

a<p>Format for age, BMI, time since meal, and FA ratios: mean (standard deviation). Format for smoking, fasting, supplements and medication: frequency (percent). Missing: BMI: 3, smoking: 1, fasting: 27, n-3 supplements: 5.</p><p><b>Abbreviations:</b> AA: arachidonic acid, ALA: alpha-linolenic acid, BMI: body mass index, EPA: eicosapentaenoic acid, h: hours, HRT: hormone replacement therapy, LA: linoleic acid, n-3 supplements: any combination of n-3 capsules/oils, cod liver oil or both, NSAIDs: non-steroidal anti-inflammatory drugs.</p

Number of differentially expressed genes (t-tests, p≤0.01).

<p><b>Abbreviations:</b> AA: arachidonic acid, ALA: alpha-linolenic acid, EPA: eicosapentaenoic acid, FA: fatty acid, LA: linoleic acid.</p

Top 10 up- and down-regulated genes associated with LA/ALA ratio (p≤0.01)^a.

a<p>Complete lists of differentially expressed genes (p≤0.01) are given in Supplemental <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067270#pone.0067270.s003" target="_blank">Table S2</a>.</p><p><b>Abbreviations:</b> ABI: Applied Biosystems, ALA: alpha-linolenic acid, LA: linoleic acid.</p

Significant overlaps between differentially expressed genes and reported gene sets in MSigDB^a.

a<p>The table is sorted by p-values with the lowest first, all p-values<0.01. Number of genes submitted for comparison was 184 for LA/ALA, 36 for AA/EPA, and 65 for n-6/n-3. Gene sets significant at p<0.05 are provided in Supplemental <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067270#pone.0067270.s006" target="_blank">Tables S5</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067270#pone.0067270.s008" target="_blank">S7</a>.</p><p><b>Abbreviations:</b> AA: arachidonic acid, ALA: alpha-linolenic acid, EPA: eicosapentaenoic acid, FA: fatty acid, K: number of genes in gene set, k: number of genes in overlap, LA: linoleic acid.</p

Gene Set Enrichment Analysis.

a<p>There were no significantly enriched gene sets related to n-6/n-3.</p><p><b>Abbreviations:</b> AA: arachidonic acid, ALA: alpha-linolenic acid, EPA: eicosapentaenoic acid, FA: fatty acid, FDR: false discovery rate, LA: linoleic acid, NES: normalized enrichment score, NOM p: nominal p-value.</p

Top 10 up- and down-regulated genes associated with AA/EPA ratio (p≤0.01)^a.

a<p>Complete lists of differentially expressed genes (p≤0.01) are given in Supplemental <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067270#pone.0067270.s004" target="_blank">Table S3</a>.</p><p><b>Abbreviations:</b> AA: arachidonic acid, ABI: Applied Biosystems, EPA: eicosapentaenoic acid.</p

Characteristics of the highest and lowest fatty acid ratio deciles^a.

a<p>Decile n = 23. Subgroups may not total 227 due to missing values.</p><p><b>Abbreviations:</b> AA: arachidonic acid, ALA: alpha-linolenic acid, BMI: body mass index, EPA: eicosapentaenoic acid, h: hours, HRT: hormone replacement therapy, LA: linoleic acid, n-3 suppl.: any combination of n-3 capsules/oils, cod liver oil or both, NSAIDs: non-steroidal anti-inflammatory drugs.</p

Top 10 up- and down-regulated genes associated with total n-6/n-3 ratio (p≤0.01)^a.

a<p>Complete lists of differentially expressed genes (p≤0.01) are given in Supplemental <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067270#pone.0067270.s005" target="_blank">Table S4</a>.</p><p><b>Abbreviations:</b> ABI: Applied Biosystems.</p

Circadian rhythm genes differentially expressed in tumour shown with KEGG PATHWAYS (modified from Kanehisa <i>et al</i>., 2008) (<i>P</i><0.05).

<p>CRY2, PER1, PER3 and NR1D1/Rev-Erb alpha that function as negative regulators of transcription are down-regulated (green) whereas both genes encoding the active transcriptional heterodimeric complex Bmal1(ARNTL):Npas2 (NPAS2) are overexpressed in mesothelioma versus normal parietal pleura. Damaged circadian rhythms may be a key to the continuous replicative force in tumour cells, and thus possible treatment targets.</p

Protein expression of selected genes, AGGF1, TYMS and MSLN by immunohistochemistry.

<p>A–C–E: normal parietal pleura. B–D–F: Biphasic mesothelioma with epithelial and sarcomarous components. A–B (x20): AGGF1(VG5Q) mRNA was overexpressed in mesothelioma, and clearly protein was expressed (brown) in both tumour components (arrows). Strong expression in normal mesothelium was seen (arrow) but the majority of endothelial and other pleural cells were negative. C–D (x40): TYMS (Thymidylate synthase) mRNA was overexpressed, also on the protein level (brown), mostly in the epithelial component (arrow) of tumour. Normal pleura was negative. E–F (x20): MSLN (Mesothelin) mRNA was not differentially expressed, that could be explained by the intense protein expression not only in epithelial tumour cells, but also in normal mesothelial and stromal cells.</p