{"doi":"10.1101/2021.05.14.444026","title":"CovidExpress: an interactive portal for intuitive investigation on SARS-CoV-2 related transcriptomes","abstract":"Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans could cause coronavirus disease 2019 (COVID-19). Since its first discovery in Dec 2019, SARS-CoV-2 has become a global pandemic and caused 3.3 million direct/indirect deaths (2021 May). Amongst the scientific community's response to COVID-19, data sharing has emerged as an essential aspect of the combat against SARS-CoV-2. Despite the ever-growing studies about SARS-CoV-2 and COVID-19, to date, only a few databases were curated to enable access to gene expression data. Furthermore, these databases curated only a small set of data and do not provide easy access for investigators without computational skills to perform analyses. To fill this gap and advance open-access to the growing gene expression data on this deadly virus, we collected about 1,500 human bulk RNA-seq datasets from publicly available resources, developed a database and visualization tool, named CovidExpress (https://stjudecab.github.io/covidexpress). This open access database will allow research investigators to examine the gene expression in various tissues, cell lines, and their response to SARS-CoV-2 under different experimental conditions, accelerating the understanding of the etiology of this disease to inform the drug and vaccine development. Our integrative analysis of this big dataset highlights a set of commonly regulated genes in SARS-CoV-2 infected lung and Rhinovirus infected nasal tissues, including OASL that were under-studied in COVID-19 related reports. Our results also suggested a potential FURIN positive feedback loop that might explain the evolutional advantage of SARS-CoV-2.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":214557,"datarank":0.5259901739366118,"base_score":2.302585092994046,"endowment":2.302585092994046,"self_citation_contribution":0.3453877639491069,"citation_network_contribution":0.18060240998750496,"self_endowment_contribution":0.3453877639491069,"citer_contribution":0.18060240998750496,"corpus_percentile":63.154637580258374,"corpus_rank":4764,"citation_count":9,"citer_count":9,"citers_with_citation_signal":5,"citers_with_endowment":5,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5333,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":342938,"name":"Wojciech Rosikiewicz","orcid":"0000-0001-7031-3430","position":1,"is_corresponding":false},{"id":324114,"name":"Jamy C. Peng","orcid":"0000-0002-4043-8475","position":2,"is_corresponding":false},{"id":105446,"name":"Thirumala‐Devi Kanneganti","orcid":"0000-0002-6395-6443","position":3,"is_corresponding":false},{"id":808072,"name":"Yawei Hui","orcid":"0000-0001-6397-3086","position":4,"is_corresponding":false},{"id":55234,"name":"Hongjian Jin","orcid":"0000-0003-3833-7170","position":5,"is_corresponding":false},{"id":178847,"name":"Dale J. Hedges","orcid":null,"position":6,"is_corresponding":false},{"id":105441,"name":"Patrick Schreiner","orcid":"0000-0001-5391-2642","position":7,"is_corresponding":false},{"id":250676,"name":"Yiping Fan","orcid":"0000-0002-8430-4620","position":8,"is_corresponding":false},{"id":55256,"name":"Gang Wu","orcid":"0000-0002-1678-5864","position":9,"is_corresponding":false},{"id":267013,"name":"Beisi Xu","orcid":"0000-0003-0099-858X","position":10,"is_corresponding":false},{"id":622875,"name":"Mohamed Nadhir Djekidel","orcid":"0000-0001-5361-1858","position":0,"is_corresponding":true}],"reference_count":89,"raw_metadata":null,"created_at":"2026-07-18T23:52:46.604690Z","pmid":"34075382","pmcid":"PMC8168395","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}