Dataset Information

GeNemo: a search engine for web-based functional genomic data.

ABSTRACT: A set of new data types emerged from functional genomic assays, including ChIP-seq, DNase-seq, FAIRE-seq and others. The results are typically stored as genome-wide intensities (WIG/bigWig files) or functional genomic regions (peak/BED files). These data types present new challenges to big data science. Here, we present GeNemo, a web-based search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets. Unlike text-based search engines, GeNemo's searches are based on pattern matching of functional genomic regions. This distinguishes GeNemo from text or DNA sequence searches. The user can input any complete or partial functional genomic dataset, for example, a binding intensity file (bigWig) or a peak file. GeNemo reports any genomic regions, ranging from hundred bases to hundred thousand bases, from any of the online ENCODE datasets that share similar functional (binding, modification, accessibility) patterns. This is enabled by a Markov Chain Monte Carlo-based maximization process, executed on up to 24 parallel computing threads. By clicking on a search result, the user can visually compare her/his data with the found datasets and navigate the identified genomic regions. GeNemo is available at www.genemo.org.

SUBMITTER: Zhang Y

PROVIDER: S-EPMC4987887 | biostudies-other | 2016 Jul

REPOSITORIES: biostudies-other

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GeNemo: a search engine for web-based functional genomic data.

Zhang Yongqing Y Cao Xiaoyi X Zhong Sheng S

Nucleic acids research 20160420 W1

A set of new data types emerged from functional genomic assays, including ChIP-seq, DNase-seq, FAIRE-seq and others. The results are typically stored as genome-wide intensities (WIG/bigWig files) or functional genomic regions (peak/BED files). These data types present new challenges to big data science. Here, we present GeNemo, a web-based search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCO ...[more]

PMID: 27098038

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Project description:BackgroundAnxiety disorders are the most prevalent mental disorders globally, with a substantial impact on quality of life. The prevalence of anxiety disorders has increased substantially following the COVID-19 pandemic, and it is likely to be further affected by a global economic recession. Understanding anxiety themes and how they change over time and across countries is crucial for preventive and treatment strategies.ObjectiveThe aim of this study was to track the trends in anxiety themes between 2004 and 2020 in the 50 most populous countries with high volumes of internet search data. This study extends previous research by using a novel search-based methodology and including a longer time span and more countries at different income levels.MethodsWe used a crowdsourced questionnaire, alongside Bing search query data and Google Trends search volume data, to identify themes associated with anxiety disorders across 50 countries from 2004 to 2020. We analyzed themes and their mutual interactions and investigated the associations between countries' socioeconomic attributes and anxiety themes using time-series linear models. This study was approved by the Microsoft Research Institutional Review Board.ResultsQuery volume for anxiety themes was highly stable in countries from 2004 to 2019 (Spearman r=0.89) and moderately correlated with geography (r=0.49 in 2019). Anxiety themes were predominantly long-term and personal, with "having kids," "pregnancy," and "job" the most voluminous themes in most countries and years. In 2020, "COVID-19" became a dominant theme in 27 countries. Countries with a constant volume of anxiety themes over time had lower fragile state indexes (P=.007) and higher individualism (P=.003). An increase in the volume of the most searched anxiety themes was associated with a reduction in the volume of the remaining themes in 13 countries and an increase in 17 countries, and these 30 countries had a lower prevalence of mental disorders (P<.001) than the countries where no correlations were found.ConclusionsInternet search data could be a potential source for predicting the country-level prevalence of anxiety disorders, especially in understudied populations or when an in-person survey is not viable.

Dataset Information

GeNemo: a search engine for web-based functional genomic data.

Publications

GeNemo: a search engine for web-based functional genomic data.

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