Ontological Analysis of Coronavirus Associated Human Genes at the COVID-19 Disease Portal.

The COVID-19 pandemic stemmed a parallel upsurge in the scientific literature about SARS-CoV-2 infection and its health burden. The Rat Genome Database (RGD) created a COVID-19 Disease Portal to leverage information from the scientific literature. In the COVID-19 Portal, gene-disease associations are established by manual curation of PubMed literature. The portal contains data for nine ontologies related to COVID-19, an embedded enrichment analysis tool, as well as links to a toolkit. Using these information and tools, we performed analyses on the curated COVID-19 disease genes. As expected, Disease Ontology enrichment analysis showed that the COVID-19 gene set is highly enriched with coronavirus infectious disease and related diseases. However, other less related diseases were also highly enriched, such as liver and rheumatic diseases. Using the comparison heatmap tool, we found nearly 60 percent of the COVID-19 genes were associated with nervous system disease and 40 percent were associated with gastrointestinal disease. Our analysis confirms the role of the immune system in COVID-19 pathogenesis as shown by substantial enrichment of immune system related Gene Ontology terms. The information in RGD's COVID-19 disease portal can generate new hypotheses to potentiate novel therapies and prevention of acute and long-term complications of COVID-19.

MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses.

Biological interpretation of a large amount of gene or protein data is complex. Ontology analysis tools are imperative in finding functional similarities through overrepresentation or enrichment of terms associated with the input gene or protein lists. However, most tools are limited by their ability to do ontology-specific and species-limited analyses. Furthermore, some enrichment tools are not updated frequently with recent information from databases, thus giving users inaccurate, outdated or uninformative data. Here, we present MOET or the Multi-Ontology Enrichment Tool (v.1 released in April 2019 and v.2 released in May 2021), an ontology analysis tool leveraging data that the Rat Genome Database (RGD) integrated from in-house expert curation and external databases including the National Center for Biotechnology Information (NCBI), Mouse Genome Informatics (MGI), The Kyoto Encyclopedia of Genes and Genomes (KEGG), The Gene Ontology Resource, UniProt-GOA, and others. Given a gene or protein list, MOET analysis identifies significantly overrepresented ontology terms using a hypergeometric test and provides nominal and Bonferroni corrected P-values and odds ratios for the overrepresented terms. The results are shown as a downloadable list of terms with and without Bonferroni correction, and a graph of the P-values and number of annotated genes for each term in the list. MOET can be accessed freely from https://rgd.mcw.edu/rgdweb/enrichment/start.html.

Small intestine mucosal adhesivity to in vivo capsule robot materials.

Multiple research groups are investigating the feasibility of miniature, swallowable, in vivo, untethered robots that are capable of traversing the small intestine for the purpose of acquiring biometrics and performing simple surgical procedures. A mathematical model of the intraluminal environment will speed the development of these so-called Robotic Capsule Endoscopes (RCEs), and to this end, the authors, in previous work, initiated a comprehensive program for characterizing both the active and passive forces exerted by the small intestine on an RCE-sized solid bolus. In this work, forces due to adhesivity between RCE materials and the mucosa are investigated. The experimental factors are adhesive modality (peel and tack), material (polycarbonate, micropatterned polydimethylsiloxane, stainless steel, and mucosa), and bowel region (proximal, middle, and distal). The mucosa is excised from a fasting pig, stored in lactated ringer's solution at 3 °C, and then tested at room temperature within 43 h of excision. The results show the mean tack strength of the mucosa to engineering materials was 0.198±0.070 mJ cm⁻². The mean peel strength was 0.055±0.016 mJ cm⁻². This study marks the first time, to the authors' knowledge, that adhesivity between small intestinal mucosa and RCE engineering materials has been measured. The adhesivity values acquired from this study will provide a valuable input into analytical and numerical models of the gastrointestinal tract, specifically models that account for the interfacial properties of the tissue.