title: MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes.
abstract: The microbiota colonized on human body is renowned as "a forgotten organ" due to its big impacts on human health and disease. Recently, microbiome studies have identified a large number of microbes differentially regulated in a variety of conditions, such as disease and diet. However, methods for discovering biological patterns in the differentially regulated microbes are still limited. For this purpose, here, we developed a web-based tool named MicroPattern to discover biological patterns for a list of microbes. In addition, MicroPattern implemented and integrated an algorithm we previously presented for the calculation of disease similarity based on disease-microbe association data. MicroPattern first grouped microbes into different sets based on the associated diseases and the colonized positions. Then, for a given list of microbes, MicroPattern performed enrichment analysis of the given microbes on all of the microbe sets. Moreover, using MicroPattern, we can also calculate disease similarity based on the shared microbe associations. Finally, we confirmed the accuracy and usefulness of MicroPattern by applying it to the changed microbes under the animal-based diet condition. MicroPattern is freely available at http://www.cuilab.cn/micropattern.
authors.affiliation: Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.|MOE Key Lab of Cardiovascular Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Ma
authors.affiliation: Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.|Department of Mathematics, Huaqiao University, 269 Huabei Road, Quanzhou, Fujian Province, 362021, China.
authors.forename: Chuanbo
authors.initials: C
authors.lastname: Huang
authors.affiliation: Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.|MOE Key Lab of Cardiovascular Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.|School of Computer Science and Engineering, Hebei University of Technology, 5340 Xiping Road, Tianjin, 300401, China.
authors.forename: Jianwei
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.|MOE Key Lab of Cardiovascular Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China.
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Cui
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D064806:Dysbiosis / Q000175:diagnosis*; D006801:Humans; D020407:Internet; D064307:Microbiota; D012984:Software