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Nucleic Acids Research Papers on Coronavirus, Tumor Expression-Methylation, Microbiome Resources

Researchers at the University of Alabama at Birmingham and the University of Wisconsin-Madison School of Medicine present an online database for compiling coronavirus-related gene, pathway, and gene signature data. The "pathways, annotated gene-lists, and gene signatures electronic repository for coronavirus" (PAGER-CoV) contains data from dozens of SARS-CoV-2 studies, the team says, including drug repositioning candidate data and host immune response clues. For their own proof-of-principle analyses, for example, the authors tapped into COVID-19-related single-cell RNA sequence data for a gene set enrichment analysis aimed at identifying lung immune responses distinguishing moderate and more severe SARS-CoV-2 infections. They argue that PAGER-CoV will be "invaluable for biomedical researchers to find molecular biology mechanisms and tailored therapeutics to treat COVID-19 patients."

A Chinese University of Hong Kong team details updates to a database called MethHC that includes DNA methylation and corresponding gene expression profiles representing nearly three dozen cancer types. Version 2.0 of the MethHC database encompasses more than 50,100 array- or RNA sequencing-based transcriptome profiles reported for samples from 33 cancer types, the researchers note, together with related DNA methylation data for some 28,047 genes and insights from more than 1,000 microRNAs. Along with additional gene regulation, somatic mutation, copy number, circulating tumor DNA, and clinical clues, the cancer transcriptome and methylome data in MethHC 2.0 platform makes it possible to "compare methylation among several cancer types, pathological stage, and cancers with or without mutations or with different copy number variations for a given gene," the authors write.

Finally, investigators from the University of Maryland School of Medicine share an update on online resources offered by the Human Microbiome Project (HMP)'s Data Coordination Center, or HMPDACC, for making data from the Human Microbiome and Integrative Human Microbiome Projects available for analyses by other researchers. The data portal currently houses multi-omic data spanning tens of thousands of samples and reference genomes profiled for phase one and phase two of HMP. The online portal "provides a unified data repository, multi-faceted search functionality, analysis pipelines, and standardized protocols to facilitate community use of HMP data," the authors write, noting that "[r]ecent efforts have been put toward making HMP data more findable, accessible, interoperable, and reusable."