{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T16:59:43Z","timestamp":1761238783142,"version":"3.41.2"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,9,22]],"date-time":"2020-09-22T00:00:00Z","timestamp":1600732800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100010803","name":"Department of Biotechnology","doi-asserted-by":"publisher","award":["BT\/PR15619\/AGIII\/103\/908\/2015"],"award-info":[{"award-number":["BT\/PR15619\/AGIII\/103\/908\/2015"]}],"id":[{"id":"10.13039\/501100010803","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>RNA-seq data analysis with rapidly advancing high-throughput sequencing technology, nowadays provides large number of transcripts or genes to perform downstream analysis including functional annotation and pathway analysis. However for the data from multiple tissues, downstream analysis with tissue-specific or tissue-enriched transcripts is highly preferable. However, there is still a need of tool for quickly performing tissue-enrichment and gene expression analysis irrespective of number of input genes or tissues at various fragments per kilobase of transcript per million fragments mapped (FPKM) thresholds. To fulfill this need, we presented a freely available R package and web-interface tool, TEnGExA, which allows tissue-enrichment analysis (TEA) for any number of genes or transcripts for any species provided only a read-count or FPKM-value matrix as input. Based on the different FPKM value and fold thresholds, TEnGExA classifies the user provided gene lists into tissue-enriched or tissue-specific transcripts along with other standard classes. By analyzing the published sample data from human, plant and microorganism, we signifies that TEnGExA can easily handle complex or large data from any species to provided tissue-enriched gene list for downstream analysis in quick time. In summary, TEnGExA is quick, easy to use and an efficient tool for TEA. The R package is freely available at https:\/\/github.com\/ubagithub\/TEnGExA\/ and the GUI web interface is accessible at http:\/\/webtom.cabgrid.res.in\/tissue_enrich\/.<\/jats:p>","DOI":"10.1093\/bib\/bbaa221","type":"journal-article","created":{"date-parts":[[2020,9,2]],"date-time":"2020-09-02T19:13:45Z","timestamp":1599074025000},"source":"Crossref","is-referenced-by-count":9,"title":["<i>TEnGExA:<\/i> an R package based tool for tissue enrichment and gene expression analysis"],"prefix":"10.1093","volume":"22","author":[{"given":"Hukam C","family":"Rawal","sequence":"first","affiliation":[{"name":"Indian Council of Agricultural Research (ICAR)-NIPB, New Delhi, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ulavappa","family":"Angadi","sequence":"additional","affiliation":[{"name":"Kalasalingam University, Krishnankoil, Srivilliputtur, Tamil Nadu, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tapan Kumar","family":"Mondal","sequence":"additional","affiliation":[{"name":"ICAR-National Institute for Plant Biotechnology, LBS Centre, IARI, New Delhi 110012, India"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,9,22]]},"reference":[{"issue":"11","key":"2021052110414134800_ref1","doi-asserted-by":"publisher","first-page":"1966","DOI":"10.1093\/bioinformatics\/bty890","article-title":"TissueEnrich: tissue-specific gene enrichment analysis","volume":"35","author":"Jain","year":"2019","journal-title":"Bioinformatics"},{"issue":"19","key":"2021052110414134800_ref2","doi-asserted-by":"publisher","first-page":"3842","DOI":"10.1093\/bioinformatics\/btz138","article-title":"deTS: tissue-specific enrichment analysis to decode tissue specificity","volume":"35","author":"Pei","year":"2019","journal-title":"Bioinformatics"},{"issue":"1","key":"2021052110414134800_ref3","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1186\/s12859-016-1229-9","article-title":"Tissue enrichment analysis for C. elegans genomics","volume":"17","author":"Angeles-Albores","year":"2016","journal-title":"BMC Bioinformatics"},{"issue":"6220","key":"2021052110414134800_ref4","doi-asserted-by":"publisher","first-page":"1260419","DOI":"10.1126\/science.1260419","article-title":"Proteomics. Tissue-based map of the human proteome","volume":"347","author":"Uhl\u00e9n","year":"2015","journal-title":"Science"},{"key":"2021052110414134800_ref5","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1016\/j.indcrop.2019.03","article-title":"Tissue specific long non-coding RNAs are involved in aroma formation of black tea","volume":"133","author":"Varshney","year":"2019","journal-title":"Ind Crops Prod"},{"issue":"D1","key":"2021052110414134800_ref6","doi-asserted-by":"publisher","first-page":"D1031","DOI":"10.1093\/nar\/gkx850","article-title":"TissGDB: tissue-specific gene database in cancer","volume":"46","author":"Kim","year":"2018","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2021052110414134800_ref7","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-015-0116-6","article-title":"Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles","volume":"13","author":"Blazie","year":"2015","journal-title":"BMC Biol"},{"key":"2021052110414134800_ref8","doi-asserted-by":"publisher","DOI":"10.1038\/s12276-018-0071-8","article-title":"Single-cell RNA sequencing technologies and bioinformatics pipelines","volume":"50","author":"Hwang","year":"2018","journal-title":"Exp Mol Med"},{"key":"2021052110414134800_ref9","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1186\/1471-2164-10-269","article-title":"Definition, conservation and epigenetics of housekeeping and tissue-enriched genes","volume":"10","author":"She","year":"2009","journal-title":"BMC Genomics"},{"issue":"9","key":"2021052110414134800_ref10","doi-asserted-by":"publisher","first-page":"449","DOI":"10.3390\/genes9090449","article-title":"A computational method for classifying different human tissues with quantitatively tissue-specific expressed genes","volume":"9","author":"Li","year":"2018","journal-title":"Genes (Basel)"},{"issue":"12","key":"2021052110414134800_ref11","doi-asserted-by":"publisher","first-page":"372","DOI":"10.3390\/genes8120372","article-title":"Tissue-specific Transcriptome analysis reveals multiple responses to salt stress in Populus euphratica seedlings","volume":"8","author":"Yu","year":"2017","journal-title":"Genes (Basel)"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/22\/3\/bbaa221\/37965491\/bbaa221.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/22\/3\/bbaa221\/37965491\/bbaa221.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,5,21]],"date-time":"2021-05-21T10:44:28Z","timestamp":1621593868000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaa221\/5909881"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,9,22]]},"references-count":11,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2021,5,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaa221","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"type":"print","value":"1467-5463"},{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2021,5]]},"published":{"date-parts":[[2020,9,22]]},"article-number":"bbaa221"}}