{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T23:22:09Z","timestamp":1776813729592,"version":"3.51.2"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2021,7,12]],"date-time":"2021-07-12T00:00:00Z","timestamp":1626048000000},"content-version":"vor","delay-in-days":11,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Takeda Pharmaceuticals"},{"name":"United States National Institutes of Health"},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["R24DK110499"],"award-info":[{"award-number":["R24DK110499"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Metatranscriptomics (MTX) has become an increasingly practical way to profile the functional activity of microbial communities in situ. However, MTX remains underutilized due to experimental and computational limitations. The latter are complicated by non-independent changes in both RNA transcript levels and their underlying genomic DNA copies (as microbes simultaneously change their overall abundance in the population and regulate individual transcripts), genetic plasticity (as whole loci are frequently gained and lost in microbial lineages) and measurement compositionality and zero-inflation. Here, we present a systematic evaluation of and recommendations for differential expression (DE) analysis in MTX.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We designed and assessed six statistical models for DE discovery in MTX that incorporate different combinations of DNA and RNA normalization and assumptions about the underlying changes of gene copies or species abundance within communities. We evaluated these models on multiple simulated and real multi-omic datasets. Models adjusting transcripts relative to their encoding gene copies as a covariate were significantly more accurate in identifying DE from MTX in both simulated and real datasets. Moreover, we show that when paired DNA measurements (metagenomic data) are not available, models normalizing MTX measurements within-species while also adjusting for total-species RNA balance sensitivity, specificity and interpretability of DE detection, as does filtering likely technical zeros. The efficiency and accuracy of these models pave the way for more effective MTX-based DE discovery in microbial communities.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The analysis code and synthetic datasets used in this evaluation are available online at http:\/\/huttenhower.sph.harvard.edu\/mtx2021.<\/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\/btab327","type":"journal-article","created":{"date-parts":[[2021,5,5]],"date-time":"2021-05-05T19:04:46Z","timestamp":1620241486000},"page":"i34-i41","source":"Crossref","is-referenced-by-count":60,"title":["Statistical approaches for differential expression analysis in metatranscriptomics"],"prefix":"10.1093","volume":"37","author":[{"given":"Yancong","family":"Zhang","sequence":"first","affiliation":[{"name":"Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health , Boston, MA 02115, USA"},{"name":"Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, MA 02115, USA"},{"name":"Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}]},{"given":"Kelsey N","family":"Thompson","sequence":"additional","affiliation":[{"name":"Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health , Boston, MA 02115, USA"},{"name":"Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, MA 02115, USA"},{"name":"Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}]},{"given":"Curtis","family":"Huttenhower","sequence":"additional","affiliation":[{"name":"Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health , Boston, MA 02115, USA"},{"name":"Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, MA 02115, USA"},{"name":"Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"},{"name":"Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health , Boston, MA 02115, USA"}]},{"given":"Eric A","family":"Franzosa","sequence":"additional","affiliation":[{"name":"Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health , Boston, MA 02115, USA"},{"name":"Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, MA 02115, USA"},{"name":"Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,7,12]]},"reference":[{"key":"2023062410305193400_btab327-B1","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/ismej.2011.95","article-title":"Active and total microbial communities in forest soil are largely different and highly stratified during decomposition","volume":"6","author":"Baldrian","year":"2012","journal-title":"ISME J"},{"key":"2023062410305193400_btab327-B2","doi-asserted-by":"crossref","first-page":"19","DOI":"10.4137\/BBI.S34610","article-title":"Use of metatranscriptomics in microbiome research","volume":"10","author":"Bashiardes","year":"2016","journal-title":"Bioinform. Biol. 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