Scripts and URLs used in database queries and web-crawling for article "Genome build information is an essential part of genomic track files"

<p>All the scripts used for web crawling, querying the databases, retrieving the files and all URLs of the files retrieved for the article "Genome build information is an essential part of genomic track files".</p

Maternal and child characteristics of exposure to different medication groups by clusters.

<p>Maternal and child characteristics of exposure to different medication groups by clusters.</p

Complex patterns of concomitant medication use: A study among Norwegian women using paracetamol during pregnancy

<div><p>Background</p><p>Studies on medication safety in pregnancy often rely on an oversimplification of medication use into exposed or non-exposed, without considering intensity and timing of use in pregnancy, or concomitant medication use. This study uses paracetamol in pregnancy as the motivating example to introduce a method of clustering medication exposures longitudinally throughout pregnancy. The aim of this study was to use hierarchical cluster analysis (HCA) to better identify clusters of medication exposure throughout pregnancy.</p><p>Methods</p><p>Data from the Norwegian Mother and Child Cohort Study was used to identify subclasses of women using paracetamol during pregnancy. HCA with customized distance measure was used to identify clusters of medication exposures in pregnancy among children at 18 months.</p><p>Results</p><p>The pregnancies in the study (N = 9 778) were grouped in 5 different clusters depending on their medication exposure profile throughout pregnancy.</p><p>Conclusion</p><p>Using HCA, we identified and described profiles of women exposed to different medications in combination with paracetamol during pregnancy. Identifying these clusters allows researchers to define exposure in ways that better reflects real-world medication usage patterns. This method could be extended to other medications and used as pre-analysis for identifying risks associated with different profiles of exposure.</p></div

Maternal characteristics for the total cohort of 9 778 women by clusters.

<p>Maternal characteristics for the total cohort of 9 778 women by clusters.</p

Child characteristics for the total cohort of 9 778 women by clusters.

<p>Child characteristics for the total cohort of 9 778 women by clusters.</p

Dendrogram and heatmap of clustering results.

<p>The x-axis of the dendrogram indicates mothers exposed to paracetamol in pregnancy, while the y-axis of the dendrogram indicates at which height mothers are clustered together. The colors of the heatmap indicate the values of pairwise distance between mothers exposed to paracetamol in pregnancy. The distance values go from 0 (indicating no distance in blue) to 60 (indicating maximum distance in yellow color).</p

Flowchart of inclusion for the final study population.

<p>Flowchart of inclusion for the final study population.</p

Enrichment of HPV integration sites inside regions marked by H3K4me3 in different cell types.

<p>Enrichment for a given cell type is calculated based on overlap between H3K4me3 chip-seq peaks for the cell type and HPV integration sites including 10kb flanks in both directions. Enrichment values are further normalized as described in Methods.</p

Relative enrichment of HPV integration sites within regions marked as DNase hypersensitive across cell types.

<p>The table shows the cell types with the ten highest and ten lowest enrichment values. A table of all 147 analyzed cells is provided at the supplementary Galaxy Page. The enrichment values are normalized in the same way as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119566#pone.0119566.t001" target="_blank">Table 1</a> (see text).</p><p>* Epidermal keratinocytes are highly specialized epithelial cells.</p><p>Relative enrichment of HPV integration sites within regions marked as DNase hypersensitive across cell types.</p

Similarity of H3K4me3 segments between different mucosal cell types.

<p>Approximately one fifth of H3K4me3 segment coverage is unique to one cell type, showing strong similarity between different mucosal cell types.</p><p>Similarity of H3K4me3 segments between different mucosal cell types.</p