{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T12:16:14Z","timestamp":1780056974789,"version":"3.54.0"},"reference-count":12,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2016,7,5]],"date-time":"2016-07-05T00:00:00Z","timestamp":1467676800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns4:p>\n                    RNA-seq analysis is becoming a standard method for global gene expression profiling. However, open and standard pipelines to perform RNA-seq analysis by non-experts remain challenging due to the large size of the raw data files and the hardware requirements for running the alignment step. Here we introduce a reproducible open source RNA-seq pipeline delivered as an IPython notebook and a Docker image. The pipeline uses state-of-the-art tools and can run on various platforms with minimal configuration overhead. The pipeline enables the extraction of knowledge from typical RNA-seq studies by generating interactive principal component analysis (PCA) and hierarchical clustering (HC) plots, performing enrichment analyses against over 90 gene set libraries, and obtaining lists of small molecules that are predicted to either mimic or reverse the observed changes in mRNA expression. We apply the pipeline to a recently published RNA-seq dataset collected from human neuronal progenitors infected with the Zika virus (ZIKV). In addition to confirming the presence of cell cycle genes among the genes that are downregulated by ZIKV, our analysis uncovers significant overlap with upregulated genes that when knocked out in mice induce defects in brain morphology. This result potentially points to the molecular processes associated with the microcephaly phenotype observed in newborns from pregnant mothers infected with the virus. In addition, our analysis predicts small molecules that can either mimic or reverse the expression changes induced by ZIKV. The IPython notebook and Docker image are freely available at:\u00a0\n                    <ns4:ext-link xmlns:ns3=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" ns3:href=\"http:\/\/nbviewer.jupyter.org\/github\/maayanlab\/Zika-RNAseq-Pipeline\/blob\/master\/Zika.ipynb\">http:\/\/nbviewer.jupyter.org\/github\/maayanlab\/Zika-RNAseq-Pipeline\/blob\/master\/Zika.ipynb<\/ns4:ext-link>\n                    \u00a0and\u00a0\n                    <ns4:ext-link xmlns:ns3=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" ns3:href=\"https:\/\/hub.docker.com\/r\/maayanlab\/zika\/\">https:\/\/hub.docker.com\/r\/maayanlab\/zika\/<\/ns4:ext-link>\n                    .\n                  <\/ns4:p>","DOI":"10.12688\/f1000research.9110.1","type":"journal-article","created":{"date-parts":[[2016,7,5]],"date-time":"2016-07-05T08:00:08Z","timestamp":1467705608000},"page":"1574","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":30,"title":["An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study"],"prefix":"10.12688","volume":"5","author":[{"given":"Zichen","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Avi","family":"Ma'ayan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2016,7,5]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"531-533","DOI":"10.1038\/483531a","article-title":"Drug development: Raise standards for preclinical cancer 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Bioinformatics."},{"key":"ref-10","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1186\/1471-2105-14-128","article-title":"Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.","volume":"14","author":"E Chen","year":"2013","journal-title":"BMC Bioinformatics."},{"key":"ref-11","article-title":"L1000CDS 2: LINCS L1000 Characteristic Direction Signature Search Engine.","author":"Q Duan","year":"2016"},{"key":"ref-12","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.56311","article-title":"Zika-RNAseq-Pipeline v0.1.","author":"Z Wang","year":"2016","journal-title":"Zenodo."}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/5-1574\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/5-1574\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/5-1574\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,12,5]],"date-time":"2018-12-05T12:46:32Z","timestamp":1544013992000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/5-1574\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,7,5]]},"references-count":12,"URL":"https:\/\/doi.org\/10.12688\/f1000research.9110.1","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.9804.r15290","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.9804.r15289","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.9804.r14924","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.9804.r15289","asserted-by":"object"},{"id-type":"doi","id":"10.5256\/f1000research.9804.r14924","asserted-by":"object"},{"id-type":"doi","id":"10.5256\/f1000research.9804.r15290","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,7,5]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/5-1574\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.9804.r14924, Ravi K. Madduri, Computation Institute, University of Chicago, Chicago, IL, USA, 21 Jul 2016, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/5-1574\/v1#referee-response-14924","order":0,"name":"referee-response-14924","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.9804.r15290, Apostolos Zaravinos, The School of Sciences, European University Cyprus, Engomi, Cyprus, 29 Jul 2016, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/5-1574\/v1#referee-response-15290","order":1,"name":"referee-response-15290","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.9804.r15289, Fredrik Pettersson, Sarbashis Das, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden, 15 Aug 2016, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/5-1574\/v1#referee-response-15289","order":2,"name":"referee-response-15289","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work is partially supported by the National Institutes of Health (NIH) grants U54HL127624, U54CA189201, and R01GM098316. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}