GlobeCorr: interactive globe-based visualization for correlation datasets.

Motivation: Increasingly complex omics datasets are being generated, along with associated diverse categories of metadata (environmental, clinical, etc.). Looking at the correlation between these variables can be critical to identify potential confounding factors and novel relationships. To date, some correlation globe software has been developed to aid investigations; however, they lack secure, dynamic visualization capability. Results: GlobeCorr.ca is a web-based application designed to provide user-friendly, interactive visualization and analysis of correlation datasets. Users load tabular data listing pairwise variables and their correlation values, and GlobeCorr creates a dynamic visualization using ribbons to represent positive and negative correlations, optionally grouped by domain/category (such as microbiome taxa against other metadata). GlobeCorr runs securely (locally on a user's computer) and provides a simple method for users to visualize and summarize complex datasets. This tool is applicable to a wide range of disciplines and domains of interest, including the bioinformatics/microbiome and metadata examples provided within. Availability and Implementation: See https://GlobeCorr.ca; Code provided under an open source MIT license: https://github.com/brinkmanlab/globecorr.

Integrative chromatin domain annotation through graph embedding of Hi-C data.

MOTIVATION: The organization of the genome into domains plays a central role in gene expression and other cellular activities. Researchers identify genomic domains mainly through two views: 1D functional assays such as ChIP-seq, and chromatin conformation assays such as Hi-C. Fully understanding domains requires integrative modeling that combines these two views. However, the predominant form of integrative modeling uses segmentation and genome annotation (SAGA) along with the rigid assumption that loci in contact are more likely to share the same domain type, which is not necessarily true for epigenomic domain types and genome-wide chromatin interactions. RESULTS: Here, we present an integrative approach that annotates domains using both 1D functional genomic signals and Hi-C measurements of genome-wide 3D interactions without the use of a pairwise prior. We do so by using a graph embedding to learn structural features corresponding to each genomic region, then inputting learned structural features along with functional genomic signals to a SAGA algorithm. We show that our domain types recapitulate well-known subcompartments with an additional granularity that distinguishes a combination of the spatial and functional states of the genomic regions. In particular, we identified a division of the previously identified A2 subcompartment such that the divided domain types have significantly varying expression levels. AVAILABILITY AND IMPLEMENTATION: https://github.com/nedashokraneh/IChDA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Relative Contribution of Obesity, Sedentary Behaviors and Dietary Habits to Sleep Duration Among Kuwaiti Adolescents.

The aim of this study was to investigate whether body mass index (BMI), eating habits and sedentary behaviours were associated with sleep duration among Kuwaiti adolescents. The study is part of the Arab Teens Lifestyle Study (ATLS), which is a school-based cross-sectional multi-center collaborative study. A sample of 906 adolescents (boys and girls) aged 14-19 years was randomly selected from 6 Kuwaiti Governances using a multistage stratified cluster sampling technique. The findings revealed that the prevalence of overweight and obesity was 50.5% in boys and 46.5% in girls. The majority of boys (76%) and of girls (74%) fell into the short sleep duration category (6 hours/day or less). Sleep duration were found to be negatively associated with BMI (girls only). Watching television (boys and girls) and working on computers (boys only) were also negatively associated with sleep duration. While the consumption of breakfast (both genders) and milk (boys only) was positively associated with sleep duration (p<0.05). In contrast, the consumption of fast foods (both genders), sugar-sweetened drinks and sweets (boys only) potatoes (girls only) were negatively associated with sleep duration (p<0.05). It can be concluded that the majority of Kuwaiti adolescents exhibit insufficient sleep duration which was associated with obesity measure, a combination of poor eating habits and more sedentary behaviors. The findings also suggest gender differences in these associations. Therefore, adequate sleep is an important modifiable risk factor to prevent obesity and was positively associated with some unhealthy lifestyle habits.