{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:29Z","timestamp":1772138009401,"version":"3.50.1"},"reference-count":83,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,1,18]],"date-time":"2021-01-18T00:00:00Z","timestamp":1610928000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,3,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The current genomics era is bringing an unprecedented growth in the amount of gene expression data, only comparable to the exponential growth of sequences in databases during the last decades. This data allow the design of secondary analyses that take advantage of this information to create new knowledge. One of these feasible analyses is the evaluation of the expression level for a gene through a series of different conditions or cell types. Based on this idea, we have developed Automatic and Serial Analysis of CO-expression, which performs expression profiles for a given gene along hundreds of heterogeneous and normalized transcriptomics experiments and discover other genes that show either a similar or an inverse behavior. It might help to discover co-regulated genes, and common transcriptional regulators in any biological model. The present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is an opportunity to test this novel approach due to the wealth of data that are being generated, which could be used for validating results. Thus, we have identified 35 host factors in the literature putatively involved in the infectious cycle of SARS-CoV viruses and searched for genes tightly co-expressed with them. We have found 1899 co-expressed genes whose assigned functions are strongly related to viral cycles. Moreover, this set of genes heavily overlaps with those identified by former laboratory high-throughput screenings (with P-value near 0). Our results reveal a series of common regulators, involved in immune and inflammatory responses that might be key virus targets to induce the coordinated expression of SARS-CoV-2 host factors.<\/jats:p>","DOI":"10.1093\/bib\/bbaa419","type":"journal-article","created":{"date-parts":[[2020,12,21]],"date-time":"2020-12-21T07:09:14Z","timestamp":1608534554000},"page":"1038-1052","source":"Crossref","is-referenced-by-count":5,"title":["Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3343-2822","authenticated-orcid":false,"given":"Antonio J","family":"P\u00e9rez-Pulido","sequence":"first","affiliation":[{"name":"Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (\u00c1rea de Gen\u00e9tica), Universidad Pablo de Olavide, 41013, Sevilla, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0874-1826","authenticated-orcid":false,"given":"Gualberto","family":"Asencio-Cort\u00e9s","sequence":"additional","affiliation":[{"name":"Data Science & Big Data Lab, Universidad Pablo de Olavide, 41013, Sevilla, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1715-8579","authenticated-orcid":false,"given":"Ana M","family":"Brokate-Llanos","sequence":"additional","affiliation":[{"name":"Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (\u00c1rea de Gen\u00e9tica), Universidad Pablo de Olavide, 41013, Sevilla, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5536-6868","authenticated-orcid":false,"given":"Gloria","family":"Brea-Calvo","sequence":"additional","affiliation":[{"name":"Centro Andaluz de Biolog\u00eda del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, 41013, Sevilla, Spain"},{"name":"CIBERER, Instituto de Salud Carlos III, 28000, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3312-0848","authenticated-orcid":false,"given":"Rosario","family":"Rodr\u00edguez-Gri\u00f1olo","sequence":"additional","affiliation":[{"name":"Dpto. de Econom\u00eda, M\u00e9todos Cuantitativos e Historia Econ\u00f3mica. Universidad Pablo de Olavide, 41013 Sevilla, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4299-7198","authenticated-orcid":false,"given":"Andr\u00e9s","family":"Garz\u00f3n","sequence":"additional","affiliation":[{"name":"Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (\u00c1rea de Gen\u00e9tica), Universidad Pablo de Olavide, 41013, Sevilla, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0111-1541","authenticated-orcid":false,"given":"Manuel J","family":"Mu\u00f1oz","sequence":"additional","affiliation":[{"name":"Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (\u00c1rea de Gen\u00e9tica), Universidad Pablo de Olavide, 41013, Sevilla, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,1,18]]},"reference":[{"key":"2021032314270171000_ref1","doi-asserted-by":"crossref","first-page":"e1423","DOI":"10.1002\/wsbm.1423","article-title":"Diversification of transcription factor\u2013DNA interactions and the evolution of gene regulatory networks","volume":"10","author":"Rogers","year":"2018","journal-title":"Wiley Interdiscip Rev Syst Biol Med"},{"key":"2021032314270171000_ref2","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1016\/j.cell.2016.09.018","article-title":"Ever-changing landscapes: transcriptional enhancers in development and evolution","volume":"167","author":"Long","year":"2016","journal-title":"Cell"},{"key":"2021032314270171000_ref3","first-page":"141","article-title":"Biological complexity and integrative levels of organization","volume":"1","author":"Lobo","year":"2008","journal-title":"Nat Edu"},{"key":"2021032314270171000_ref4","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1038\/nrg3207","article-title":"Transcription factors: from enhancer binding to developmental control","volume":"13","author":"Spitz","year":"2012","journal-title":"Nat Rev Genet"},{"key":"2021032314270171000_ref5","first-page":"D77","article-title":"Expression atlas update: from tissues to single cells","volume":"48","author":"Papatheodorou","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2021032314270171000_ref6","doi-asserted-by":"crossref","first-page":"1134","DOI":"10.1038\/nsmb.1680","article-title":"A two-pronged strategy to suppress host protein synthesis by SARS coronavirus Nsp1 protein","volume":"16","author":"Kamitani","year":"2009","journal-title":"Nat Struct Mol Biol"},{"key":"2021032314270171000_ref7","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.1126\/science.abc8665","article-title":"Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2","volume":"369","author":"Thoms","year":"2020","journal-title":"Science"},{"key":"2021032314270171000_ref8","doi-asserted-by":"crossref","first-page":"405","DOI":"10.2217\/fvl-2018-0008","article-title":"Post-translational modifications of coronavirus proteins: roles and function","volume":"13","author":"Fung","year":"2018","journal-title":"Future Virol"},{"key":"2021032314270171000_ref9","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.3201\/eid2607.200282","article-title":"High contagiousness and rapid spread of severe acute respiratory syndrome coronavirus 2","volume":"26","author":"Sanche","year":"2020","journal-title":"Emerg Infect Dis"},{"key":"2021032314270171000_ref10","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.3390\/v4061011","article-title":"Mechanisms of coronavirus cell entry mediated by the viral spike protein","volume":"4","author":"Belouzard","year":"2012","journal-title":"Viruses"},{"key":"2021032314270171000_ref11","doi-asserted-by":"crossref","first-page":"2794","DOI":"10.3390\/v7062747","article-title":"Dynamics of virus-receptor interactions in virus binding, signaling, and endocytosis","volume":"7","author":"Boulant","year":"2015","journal-title":"Viruses"},{"key":"2021032314270171000_ref12","doi-asserted-by":"crossref","first-page":"557","DOI":"10.3390\/v4040557","article-title":"Ready, set, fuse! 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