scholarly journals GREG—studying transcriptional regulation using integrative graph databases

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Songqing Mei ◽  
Xiaowei Huang ◽  
Chengshu Xie ◽  
Antonio Mora
Keyword(s):  
Chronic Obstructive ◽  
Graph Database ◽  
Graph Databases ◽  
Exploratory Research ◽  
Obstructive Pulmonary Disease ◽  
Web Resource ◽  
Chromatin Interactions ◽  
Non Coding Rna ◽  
Long Non Coding Rna ◽  
Single Graph

Abstract A gene regulatory process is the result of the concerted action of transcription factors, co-factors, regulatory non-coding RNAs (ncRNAs) and chromatin interactions. Therefore, the combination of protein–DNA, protein–protein, ncRNA–DNA, ncRNA–protein and DNA–DNA data in a single graph database offers new possibilities regarding generation of biological hypotheses. GREG (The Gene Regulation Graph Database) is an integrative database and web resource that allows the user to visualize and explore the network of all above-mentioned interactions for a query transcription factor, long non-coding RNA, genomic range or DNA annotation, as well as extracting node and interaction information, identifying connected nodes and performing advanced graphical queries directly on the regulatory network, in a simple and efficient way. In this article, we introduce GREG together with some application examples (including exploratory research of Nanog’s regulatory landscape and the etiology of chronic obstructive pulmonary disease), which we use as a demonstration of the advantages of using graph databases in biomedical research. Database URL: https://mora-lab.github.io/projects/greg.html, www.moralab.science/GREG/

scholarly journals Enhancer-driven chromatin interactions during development promote escape from silencing by a long non-coding RNA

2011 ◽  
Vol 4 (1) ◽  
pp. 21 ◽  
Author(s):  
Lisa Korostowski ◽  
Anjali Raval ◽  
Gillian Breuer ◽  
Nora Engel
Keyword(s):  
Chromatin Interactions ◽  
Non Coding Rna ◽  
Long Non Coding Rna

scholarly journals Long-range chromatin interactions at the mouse Igf2/H19 locus reveal a novel paternally expressed long non-coding RNA

2011 ◽  
Vol 39 (14) ◽  
pp. 5893-5906 ◽  
Author(s):  
Franck Court ◽  
Marion Baniol ◽  
Hélène Hagege ◽  
Julie Sandrine Petit ◽  
Marie-Noëlle Lelay-Taha ◽  
...  
Keyword(s):  
Long Range ◽  
Chromatin Interactions ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Oral and Oropharyngeal Sensory Function in Adults With Chronic Obstructive Pulmonary Disease

2020 ◽  
Vol 29 (2) ◽  
pp. 864-872
Author(s):  
Fernanda Borowsky da Rosa ◽  
Adriane Schmidt Pasqualoto ◽  
Catriona M. Steele ◽  
Renata Mancopes
Keyword(s):  
Chronic Obstructive Pulmonary Disease ◽  
Oral Cavity ◽  
Pulmonary Disease ◽  
Thermal Sensation ◽  
Sensory Function ◽  
Control Group ◽  
Chronic Obstructive ◽  
Obstructive Pulmonary Disease ◽  
Age Related ◽  
Copd Patients

Introduction The oral cavity and pharynx have a rich sensory system composed of specialized receptors. The integrity of oropharyngeal sensation is thought to be fundamental for safe and efficient swallowing. Chronic obstructive pulmonary disease (COPD) patients are at risk for oropharyngeal sensory impairment due to frequent use of inhaled medications and comorbidities including gastroesophageal reflux disease. Objective This study aimed to describe and compare oral and oropharyngeal sensory function measured using noninstrumental clinical methods in adults with COPD and healthy controls. Method Participants included 27 adults (18 men, nine women) with a diagnosis of COPD and a mean age of 66.56 years ( SD = 8.68). The control group comprised 11 healthy adults (five men, six women) with a mean age of 60.09 years ( SD = 11.57). Spirometry measures confirmed reduced functional expiratory volumes (% predicted) in the COPD patients compared to the control participants. All participants completed a case history interview and underwent clinical evaluation of oral and oropharyngeal sensation by a speech-language pathologist. The sensory evaluation explored the detection of tactile and temperature stimuli delivered by cotton swab to six locations in the oral cavity and two in the oropharynx as well as identification of the taste of stimuli administered in 5-ml boluses to the mouth. Analyses explored the frequencies of accurate responses regarding stimulus location, temperature and taste between groups, and between age groups (“≤ 65 years” and “> 65 years”) within the COPD cohort. Results We found significantly higher frequencies of reported use of inhaled medications ( p < .001) and xerostomia ( p = .003) in the COPD cohort. Oral cavity thermal sensation ( p = .009) was reduced in the COPD participants, and a significant age-related decline in gustatory sensation was found in the COPD group ( p = .018). Conclusion This study found that most of the measures of oral and oropharyngeal sensation remained intact in the COPD group. Oral thermal sensation was impaired in individuals with COPD, and reduced gustatory sensation was observed in the older COPD participants. Possible links between these results and the use of inhaled medication by individuals with COPD are discussed.

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