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DMPs on chromosome X. The location data: Illumina probe ID, chromosome, position, strand, UCSC gene symbol, UCSC genetic feature and regulatory feature, are shown alongside the methylation statistics: mean difference in beta, the p values and the BH-adjusted p values. DMPs associated to either PABPC5 or MIR223 are indicated in bold. (XLSX 12 kb

Rotational forceps versus manual rotation and direct forceps:a retrospective cohort study

Probability of type 2 diabetes by age in men (A) and women (B). (DOC 34 kb

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Additional file 2: Figure S1. Relative blood cell type distribution estimate in CMA patients and controls. CD8T: CD8+ T cells; CD4T: CD4+ T cells; NK: natural killer cells; Bcell: B cells; Mono: monocytes; Gran: granulocytes

Additional file 3: Figure S2. of Peripheral blood methylation profiling of female Crohn’s disease patients

DMP-distribution per genetic feature and per chromosome. a) Comparison of the probe distribution on the 450k versus the DMP distribution per genetic feature where the different colors represent the different genetic features. The numbers along the barplot represent the percentages of the 450k probes (top) or DMPs (bottom) per genetic feature. Significantly different DMP-distributions are indicated in bold red with the asterisks indicating the level of significance as found in Additional file 5: Table S3 (*: p < 0.05, **: p < 0.01, ***: p < 0.001, ****:p < 0.0001). b) For each genetic feature the percentage hypo- and hypermethylated DMPs is indicated with barplots in black and gray respectively. (PDF 54 kb

Additional file 2: Table S1. of Peripheral blood methylation profiling of female Crohn’s disease patients

Annotated data for the DMPs passing BH correction for the hypothesis-free approach. The location data: Illumina probe ID, chromosome, position, strand, UCSC gene symbol, UCSC genetic feature and regulatory feature, are shown along with the methylation statistics: mean beta difference, the p values and the BH-adjusted p. (XLSX 403 kb

Additional file 6: Figure S3. of Peripheral blood methylation profiling of female Crohn’s disease patients

Differentially methylated regions. Plots of the methylation levels of the DMRs nearest to: a) HLA-J, b) MOV10L1, c) LINC00612, c) SHANK2, d) APOBEC1, e) OR2L13 and f) TACSTD2 from the 450k (“450K”) superposed onto the RefSeq gene (“RefSeq gene”), the CpG island (“CGI”) and the transcription factor binding sites (“TFBS”), as retrieved from the UCSC Genome Browser. The red transparent rectangle indicates the DMR as reported by bumphunter. (PDF 420 kb

Additional file 1: Figure S1. of Peripheral blood methylation profiling of female Crohn’s disease patients

Exploratory data analysis of putative biological confounders. a) Variance explained per principal component based on our 450k data (turquoise triangles) versus randomly generated data (red circles). b) Dot-boxplot of the cellular composition as estimated by the Houseman algorithm [22, 23]. c) Pearson correlation coefficient (R2) of each blood cell proportion with the principal components. The statistically significant correlations are indicated in turquoise, whereas statistically non-significant associations are indicated in red. Similar correlations were calculated for d) age and e) anti-TNF usage. (PDF 119 kb

Additional file 8: Figure S4. of Peripheral blood methylation profiling of female Crohn’s disease patients

MiSeq validation. a) Correlation of the methylation levels obtained from 450k and MiSeq. Each color represents the gene associated to the plotted CpG. Visualization of the methylation levels in beta of the DMPs obtained from the 450k (“450K”) compared to the methylation levels obtained from MiSeq sequencing (“MiSEQ”) superposed onto the RefSeq gene (“RefSeq gene”) for b) TNFSF4, c) IL10/IL19, and d) ORMDL3. (PDF 146 kb

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Additional file 1: Tables

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Additional file 4: Figure S3. Categorical time span between vaccination and blood drawing (DNA) of CMA cases and controls