Electric Mobility Shift Assay (EMSA) for four sites in the promoter for Neuropeptide S Receptor 1 gene (<i>NPSR1</i>).

<p>The experiment was performed three separate times using nuclear protein extracts from two different cell types (Colo205 and HEK293). Data presented here is a representative gel using nuclear extract from Colo205. Data was similar for nuclear cell extracts from both cell lines. The sites studied included CpG site 2 coinciding with rs2168890 in a predicted HMX2 binding site, CpG site 3 in a predicted STAT1 binding site, CpG site 8 coinciding with rs2530547 in a predicted binding site for MYB, and CpG site 9 coinciding with rs887020 in a predicted binding site for AP1. Arrows indicates sites showing differential binding.</p

DNA methylation status compared between asthma cases and controls in the BAMSE cohort (n = 546) using adjusted linear regression models.

*<p>Only homozygous carriers of the allele (rs2168891) creating a CpG site were included in the analyses of CpG site 1 (Asthma ever n _{cases/controls} = 236/234, Allergic asthma n _{cases/controls} = 120/234, Non-allergic asthma n _{cases/controls} = 116/234, Current asthma n _{cases/controls} = 103/234).</p>**<p>Only homozygous carriers of the allele (rs2168890) creating a CpG site were included in the analyses of CpG site 2 (Asthma ever n _{cases/controls} = 196/201, Allergic asthma n _{cases/controls} = 94/201, Non-allergic asthma n _{cases/controls} = 201/201, Current asthma n _{cases/controls} = 89/201).</p>†<p>p-value for crude linear regression model.</p>††<p>p-value for linear regression model adjusted for gender, age at blood sampling and plate used for sodium-bisulfite treatment.</p

Neuropeptide S Receptor 1 gene (<i>NPSR1</i>) DNA methylation levels in isolated cells from peripheral blood.

<p>Peripheral blood donations were obtained from six healthy adult male donors. Data were obtained using the Illumina Infinium 450K bead array and the M-value represents methylation degree <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053877#pone.0053877-Reinius1" target="_blank">[25]</a>. Dark grey bars represent lymphoid cells, light grey bars myeloid cells and black bar whole blood. TSS – Transcription start site.</p

The effect of respiratory phenotypes and lifestyle on the levels of DNA methylation in the <i>NPSR1</i> promoter region covering CpG site 1 to 12 in adults from the BIOAIR study (n = 171) using adjusted linear regression models.

<p>COPD – Chronic Obstructive Pulmonary Disease, BMI – Body Mass Index, FEV₁ – Forced Expiratory Volume in 1 second, FVC – Forced Vital Capacity. Mild asthma patients were used as reference in the comparison to severe asthma and COPD. P: p-value for linear regression model adjusted for age, gender and country of origin. Age and gender were also adjusted for asthma and other obstructive airway disease (mild asthma, severe asthma or COPD).</p>*<p>Data analyzed in homozygous carriers of the C allele only (n_{mild asthma/severe asthma/COPD} = 47/56/44),</p>**<p>Data analyzed in homozygous carriers of the C allele only (n_{mild asthma/severe asthma/COPD} = 38/45/33),</p>†<p>Data analyzed in homozygous carriers of the C allele only (n_{mild asthma/severe asthma/COPD} = 16/27/19),</p>††<p>Data analyzed in homozygous carriers of the G allele only (n_{mild asthma/severe asthma/COPD} = 10/20/10).</p

The promoter region of the Neuropeptide S Receptor 1 gene (<i>NPSR1</i>).

<p>Polymorphisms are marked by triangles, transcription factor binding sites are underlined and CpG sites are shaded in gray. Green color of the transcription factor indicates neurologically associated factors, blue indicates immunologically associated factors, and black indicates general factors.</p

Characteristics of the BIOAIR study population (n = 171).

<p>COPD - Chronic Obstructive Pulmonary Disease, BMI – Body Mass Index, FEV₁ – Forced Expiratory Volume in 1 second, FVC – Forced Vital Capacity. Data are presented as mean ± standard deviation. P-values were calculated using ANOVA for continuous variables and chi square test for distributions.</p>1<p>one individual with missing data,</p>2<p>five individuals with missing data,</p>3<p>two individuals with missing data,</p>4<p>seven individuals with missing data,</p>5<p>three individuals with missing data.</p

Visualization of co-occurring factors in rules for allergic eczema, asthma and atopic sensitization in PARSIFAL.

<p>Rule networks for (<b>A</b>-<b>B</b>) allergic eczema, (<b>C</b>-<b>D</b>) asthma and (<b>E</b>-<b>F</b>) atopic sensitization; affected and unaffected, respectively. Conditions that occur in the rules are on the outer ring, and co-occurrences of conditions in the rules are illustrated by ribbons across the circle connecting the conditions. The ribbon color indicates high (red) to low (grey) scores. The width of the edges is proportional to the number of correctly classified children.</p

<i>TGM1</i>, <i>TGM3</i> and <i>TGM5</i> gene expression in the skin of AD patients and healthy controls.

<p>TGM transcript levels (A, E and I) of healthy controls (HC, n = 10) non lesional skin of AD patients (NL, n = 7) and lesional skin from AD patients (L, n = 10). Horizontal bars represent median values in each group and data is presented on a logaritmic scale. For IHC analysis of the TG protein expression, skin sections from nine AD patients and ten healthy controls were stained. Representative staining from one healthy control and one patient is shown in the figure for TG1 (B–D), TG3 (F–H) and TG5 (J–L) expression. Scale bar represents 50 µm.</p

Combinations of genetic variants and/or environmental factors in relation to allergy and asthma in PARSIFAL.

<p>Odds ratios are shown for the top-hits rules identified for (<b>A</b>) allergic eczema; affected^1-10 and unaffected^58-67 (<b>B</b>) asthma; affected^1-10 and unaffected^44-53 and (<b>C</b>) atopic sensitization; affected^1-10 and unaffected^37-46. The odds ratios were calculated for children that fulfill all conditions in the rule using all other children as reference.</p

Analysis methodology for factors related to childhood allergy in the epidemiologic studies BAMSE and PARSIFAL.

<p>Allergy phenotypes were modeled based on genetic and exposure data to identify (<b>A</b>) rules using gene and (<b>B</b>) gene and environment data. MCFS selected significant predictors of a phenotype, which was used to generate rules by ROSETTA. First model used 110 SNPs in BAMSE and PARSIFAL, while the second model included both genetic and exposure data in PARSIFAL, using BAMSE for validation when applicable.</p