{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:07Z","timestamp":1772138047287,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,7,21]],"date-time":"2021-07-21T00:00:00Z","timestamp":1626825600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"German Centre for Infection Research, TTU Malaria","award":["TTU 03.813"],"award-info":[{"award-number":["TTU 03.813"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>\u2002<\/jats:title>\n                    <jats:p>The increasing number of single cell and bulk RNAseq datasets describing complex gene expression profiles in different organisms, organs or cell types calls for an intuitive tool allowing rapid comparative analysis. Here, we present Swift Profiling Of Transcriptomes (SPOT) as a web tool that allows not only differential expression analysis but also fast ranking of genes fitting transcription profiles of interest. Based on a heuristic approach the spot algorithm ranks the genes according to their proximity to the user-defined gene expression profile of interest. The best hits are visualized as a table, bar chart or dot plot and can be exported as an Excel file. While the tool is generally applicable, we tested it on RNAseq data from malaria parasites that undergo multiple stage transformations during their complex life cycle as well as on data from multiple human organs during development and cell lines infected by SARS-CoV-2. SPOT should enable non-bioinformaticians to easily analyse their own and any available dataset.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SPOT is freely available for (academic) use at: https:\/\/frischknechtlab.shinyapps.io\/SPOT\/ and https:\/\/github.com\/EliasFarr\/SPOT.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab541","type":"journal-article","created":{"date-parts":[[2021,7,20]],"date-time":"2021-07-20T07:09:39Z","timestamp":1626764979000},"page":"284-285","source":"Crossref","is-referenced-by-count":1,"title":["SPOT: a web-tool enabling swift profiling of transcriptomes"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4441-6513","authenticated-orcid":false,"given":"Elias B","family":"Farr","sequence":"first","affiliation":[{"name":"Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School , Heidelberg 69120, Germany"}]},{"given":"Julia M","family":"Sattler","sequence":"additional","affiliation":[{"name":"Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School , Heidelberg 69120, Germany"},{"name":"German Center for Infection Research (DZIF) , Heidelberg 69120, Germany"}]},{"given":"Friedrich","family":"Frischknecht","sequence":"additional","affiliation":[{"name":"Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School , Heidelberg 69120, Germany"},{"name":"German Center for Infection Research (DZIF) , Heidelberg 69120, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,7,21]]},"reference":[{"key":"2023020108392729500_btab541-B1","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/s41586-019-1338-5","article-title":"Gene expression across mammalian organ development","volume":"571","author":"Cardoso-Moreira","year":"2019","journal-title":"Nature"},{"key":"2023020108392729500_btab541-B7","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1186\/s13059-015-0844-5","article-title":"MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data","volume":"16","author":"Finak","year":"2015","journal-title":"Genome Biol"},{"key":"2023020108392729500_btab541-B2","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1186\/s12859-018-2486-6","article-title":"iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data","volume":"19","author":"Ge","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2023020108392729500_btab541-B8","first-page":"184","article-title":"Integrated analysis of multimodal single-cell data","volume":"13","author":"Hao","year":"2020","journal-title":"Cell"},{"key":"2023020108392729500_btab541-B3","doi-asserted-by":"crossref","first-page":"eaaw2619","DOI":"10.1126\/science.aaw2619","article-title":"The Malaria cell atlas: single parasite transcriptomes across the complete Plasmodium life cycle","volume":"365","author":"Howick","year":"2019","journal-title":"Science"},{"key":"2023020108392729500_btab541-B9","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023020108392729500_btab541-B4","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":"2023020108392729500_btab541-B5","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1186\/s12864-019-6073-7","article-title":"GENAVi: a shiny web application for gene expression normalization, analysis and visualization","volume":"20","author":"Reyes","year":"2019","journal-title":"BMC Genomics"},{"key":"2023020108392729500_btab541-B6","doi-asserted-by":"crossref","first-page":"102151","DOI":"10.1016\/j.isci.2021.102151","article-title":"Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy","volume":"24","author":"Wyler","year":"2021","journal-title":"iScience"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab541\/39555253\/btab541.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/1\/284\/49006507\/btab541.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/1\/284\/49006507\/btab541.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T14:55:24Z","timestamp":1675263324000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/1\/284\/6325080"}},"subtitle":[],"editor":[{"given":"Jan","family":"Gorodkin","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,7,21]]},"references-count":9,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab541","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.03.03.433767","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,1]]},"published":{"date-parts":[[2021,7,21]]}}}