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Biol."],"published-print":{"date-parts":[[2015,3]]},"abstract":"<jats:p>Mining relationships between microbes and the environment they live in are crucial to understand the intrinsic mechanisms that govern cycles of carbon, nitrogen and energy in a microbial community. Building upon next\u2010generation sequencing technology, the selective capture of 16S rRNA genes has enabled the study of co\u2010occurrence patterns of microbial species from the viewpoint of complex networks, yielding successful descriptions of phenomena exhibited in a microbial community. However, since the effects of such environmental factors as temperature or soil conditions on microbes are complex, reliance on the analysis of co\u2010occurrence networks alone cannot elucidate such complicated effects underlying microbial communities. In this study, we apply a statistical method, which is called Boolean implications for metagenomic studies (BIMS) for extracting Boolean implications (IF\u2010THEN relationships) to capture the effects of environmental factors on microbial species based on 16S rRNA sequencing data. We first demonstrate the power and effectiveness of BIMS through comprehensive simulation studies and then apply it to a 16S rRNA sequencing dataset of real marine microbes. Based on a total of 6,514 pairwise relationships identified at a low false discovery rate (FDR) of 0.01, we construct a Boolean implication network between operational taxonomic units (OTUs) and environmental factors. Relationships in this network are supported by literature, and, most importantly, they bring biological insights into the effects of environmental factors on microbes. We next apply BIMS to detect three\u2010way relationships and show the possibility of using this strategy to explain more complex relationships within a microbial community.<\/jats:p>","DOI":"10.1007\/s40484-014-0037-3","type":"journal-article","created":{"date-parts":[[2015,2,17]],"date-time":"2015-02-17T11:41:58Z","timestamp":1424173318000},"page":"127-141","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Constructing a Boolean implication network to study the interactions between environmental factors and OTUs"],"prefix":"10.1002","volume":"2","author":[{"given":"Congmin","family":"Zhu","sequence":"first","affiliation":[{"name":"<!--1--> MOE Key Laboratory of Bioinformatics and Bioinformatics Division Center for Synthetic &amp; Systems Biology TNLIST\/ Department of Automation Tsinghua University Beijing 100084 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rui","family":"Jiang","sequence":"additional","affiliation":[{"name":"<!--1--> MOE Key Laboratory of Bioinformatics and Bioinformatics Division Center for Synthetic &amp; Systems Biology TNLIST\/ Department of Automation Tsinghua University Beijing 100084 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ting","family":"Chen","sequence":"additional","affiliation":[{"name":"<!--1--> MOE Key Laboratory of Bioinformatics and Bioinformatics Division Center for Synthetic &amp; Systems Biology TNLIST\/ Department of Automation Tsinghua University Beijing 100084 China"},{"name":"<!--2--> Computational and Molecular Biology Program University of Southern California Loa Angles CA 90089 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2015,3]]},"reference":[{"key":"e_1_2_8_2_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000667"},{"key":"e_1_2_8_3_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.104521.109"},{"key":"e_1_2_8_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/mr.59.1.143-169.1995"},{"key":"e_1_2_8_5_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.276.5313.734"},{"key":"e_1_2_8_6_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.57.030502.090759"},{"key":"e_1_2_8_7_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2012.00347"},{"key":"e_1_2_8_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.6.2541\u20102547.2000"},{"key":"e_1_2_8_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.69.10.6235\u20106242.2003"},{"key":"e_1_2_8_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jep.2007.08.038"},{"key":"e_1_2_8_11_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00284\u2010009\u20109398\u20107"},{"key":"e_1_2_8_12_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462\u20102920.2009.02062.x"},{"key":"e_1_2_8_13_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2011.24"},{"key":"e_1_2_8_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.178.3.591-599.1996"},{"key":"e_1_2_8_15_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms15058878"},{"key":"e_1_2_8_16_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0005299"},{"key":"e_1_2_8_17_2","doi-asserted-by":"publisher","DOI":"10.1136\/gut.2005.073817"},{"key":"e_1_2_8_18_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature11450"},{"key":"e_1_2_8_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3182"},{"key":"e_1_2_8_20_2","doi-asserted-by":"publisher","DOI":"10.1186\/1752\u20100509\u20107\u2010S4\u2010S11"},{"key":"e_1_2_8_21_2","first-page":"4","article-title":"Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data","author":"Eren A. 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