Ming Zhao, Xiwen Xiong, Kaiqun Ren, Bing Xu, Meng Cheng, Chinmayi Sahu, Kaichun Wu, Yongzhan Nie, Zan Huang, Richard S. Blumberg, Xiaonan Han, Hai‐Bin Ruan,
... Fig 5A). Linear discriminant analysis (LDA) effect size (LEfSe) highlighted differentially abundant taxonomic clades (Fig EV4B). The ... 5). B. Differentially abundant taxomonic clades analyzed by LEfSe. C, D. Abundance histogram plots of taxonomic groups detected by LEfSe that were downregulated (C) or upregulated (D) in ... Vil-Ogt KO mice that were identified by LEfSe. Regions in red indicate clades that were enriched ...
Tópico(s): Immune cells in cancer
2018 - Springer Nature | EMBO Molecular Medicine
Melody Smith, Eric R. Littmann, John Slingerland, Annelie Clurman, Ann E. Slingerland, Ying Taur, Jonathan U. Peled, Jae H. Park, Roisin E. O’Cearbhaill, Sham Mailankody, M. Lia Palomba, Elizabeth Halton, Claudia Diamonte, Renier J. Brentjens, Eric G. Pamer, Marcel R.M. van den Brink,
... 1 to 4. Linear discriminant analysis effect size (LEfSe) identified differentially abundant bacteria between groups with a ... underlying diagnosis, which included hematologic and solid malignancies. LEfSe revealed increased representation of bacterial taxa in the ... 1 to 4. Linear discriminant analysis effect size (LEfSe) identified differentially abundant bacteria between groups with a ... underlying diagnosis, which included hematologic and solid malignancies. LEfSe revealed increased representation of bacterial taxa in the ...
Tópico(s): Microscopic Colitis
2019 - Elsevier BV | Biology of Blood and Marrow Transplantation
Jean‐Luc C. Mougeot, Micaela F. Beckman, Holden C. Langdon, Rajesh V. Lalla, Michael T. Brennan, Farah K. Bahrani Mougeot,
... were compared using PERMANOVA (pMonte Carlo < 0.05). LEfSe discriminant analysis was performed to identify differentiating taxa ( ... and HC patients, respectively, regardless of antibiotics treatment. LEfSe analysis identified 43 and 44 distinctive species for ... group, 26 periodontal disease-associated species identified by LefSe had a higher average RA compared to HNC ... Whitney U-test, p < 0.05). Of 43 LEfSe-identified species in HPV+ group, 31 had a ...
Tópico(s): Salivary Gland Disorders and Functions
2022 - Frontiers Media | Frontiers in Microbiology
Richard G. Brown, M. Al‐Memar, Julian R. Marchesi, Yun Sok Lee, Ann Smith, Denise Chan, Holly Lewis, Lindsay Kindinger, Vasso Terzidou, T. Bourne, Phillip R. Bennett, David A. MacIntyre,
... each of the 5 gestational age windows. The LEfSe method29Segata N. Izard J. Waldron L. Gevers D. ... as discriminatory between the 2 outcome groups by LEfSe was calculated by Mann-Whitney. To assess the ... 65vs Control; 10, P = 0.0086) (Fig 2). LEfSe analysis of differentially abundant taxonomic features between PPROM ...
Tópico(s): Urinary Tract Infections Management
2018 - Elsevier BV | Translational research
Zeyu Zhang, Yang Xiao, Yabin Zhan, Zengqiang Zhang, Youzhou Liu, Yuquan Wei, Ting Xu, Ji Li,
... respectively, Figure 2H,I). The LDA effect size (LEfSe) analysis demonstrated that Flavobacterium, Sphingomonadales, xanthomnadaccae, and Rhizobiom ... the genus level in different treatments based on Lefse analysis. Results showed that Bacillales were enriched in ... used to explore the most discriminating OTUs using LEfSe and DESeq2, respectively [55]. Three screening criteria were ...
Tópico(s): Plant Parasitism and Resistance
2022 - Wiley | iMeta
Ali H. Zaidi, Muhammad Yogi Pratama, Ashten N. Omstead, Anastasia Gorbonova, Rubab Mansoor, Rachael Kreft, Blair A. Jobe, Patrick Wagner, Ronan J. Kelly, Ajay Goel,
... Followed by the Linear Discriminant Analysis effect size (LEfSe) method to identify microbial profiles between groups. Logistic ... gastroesophageal reflux (GERD) vs other patient groups. Interestingly, LEfSe analysis identified a complete loss of Lactobacillus (L. ... gastroesophageal reflux (GERD) vs other patient groups. Interestingly, LEfSe analysis identified a complete loss of Lactobacillus (L. ...
Tópico(s): Gastric Cancer Management and Outcomes
2022 - Springer Nature | British Journal of Cancer
Fang Chang, Shishi He, Chenyuan Dang,
... The application of Linear discriminant analysis Effect Size (LEfSe) can help find good biomarkers. Based on the ... groups based on LDA scores. To sum up, LEfSe provided the convenience for identifying genomic biomarkers that ...
Tópico(s): Genetics, Bioinformatics, and Biomedical Research
2022 - MyJOVE | Journal of Visualized Experiments
Fang Chang, Shishi He, Chenyuan Dang,
... The application of Linear discriminant analysis Effect Size (LEfSe) can help find good biomarkers. Based on the ... groups based on LDA scores. To sum up, LEfSe provided the convenience for identifying genomic biomarkers that ...
Tópico(s): Genetics, Bioinformatics, and Biomedical Research
2022 - MyJOVE | Journal of Visualized Experiments
Mahin Ghorbani, Daniel Ferreira, Silvia Maioli,
... Metaphlan3 pipeline and linear discriminant analysis effect size (LEfSe) analysis were utilized for the bioinformatics process and ... false discovery rate for all biomarkers identified by LEfSe. The CombiROC model was employed to determine the discriminatory power of the viral signatures identified by LEfSe. Results Compared to HCs, the gut virome profiles ...
Tópico(s): Epigenetics and DNA Methylation
2023 - BioMed Central | Alzheimer s Research & Therapy
John R. Lee, Thangamani Muthukumar, Darshana Dadhania, Nora C. Toussaint, Lilan Ling, Eric G. Pamer, Manikkam Suthanthiran,
... two groups, and linear discriminant analysis effect size (LEfSe) method revealed that Bacteroides, Ruminococcus, Coprococcus, and Dorea ... the no AR group (N=23) and the LEfSe method revealed significant differences between the two groups. ...
Tópico(s): Metabolism and Genetic Disorders
2014 - Wolters Kluwer | Transplantation
Eileen Dareng, Bing Ma, Ayo Famooto, Sally N Akarolo-Anthony, Richard Offiong, Olugbemi T. Olaniyan, Patrick Dakum, Cosette M. Wheeler, Doug Fadrosh, Hao Yang, Pawel Gajer, Rebecca M. Brotman, Jacques Ravel, Clement Adebamowo,
... infection, and the Linear Discriminant Analysis effect size (LEfSe) algorithm to characterize bacteria associated with prevalent hrHPV ... dominated by proteobacteria) in 2·9% of participants. LEfSe analysis suggested an association between prevalent hrHPV infection ...
Tópico(s): Gut microbiota and health
2015 - Cambridge University Press | Epidemiology and Infection
Jasmohan S. Bajaj, Naga S. Betrapally, Patrick M. Gillevet,
... we performed linear discriminant analysis (LDA) effect size (LEfSe)12 after classifying them into healthy, compensated and decompensated subjects. LEFSe uses a factorial Kruskal–Wallis and LDA test ...
Tópico(s): Gut microbiota and health
2015 - Nature Portfolio | Nature
Annika Wahlström, Petia Kovatcheva‐Datchary, Marcus Ståhlman, Muhammad-Tanweer Khan, Fredrik Bäckhed, Hanns‐Ulrich Marschall,
... 1.8.0. Linear discriminant analysis effect size (LEfSe) algorithm (13.Segata N. Izard J. Waldron L. ... with mouse and human microbiota, we applied an LEfSe algorithm (13.Segata N. Izard J. Waldron L. ...
Tópico(s): Pharmacological Effects and Toxicity Studies
2016 - Elsevier BV | Journal of Lipid Research
Daniel A. Shoskes, Jessica Altemus, A. Scott Polackwich, Barbara Tucky, Hannah Wang, Charis Eng,
... bioinformatic analyses used principal coordinate analysis (PCoA)/MacQIIME, LEfSe, and PiCRUSt algorithms.Patients and controls were similar ... noted for neurologic/systemic domains (P = .06), whereas LEfSe identified differences associated with each of the 6 ...
Tópico(s): Pelvic floor disorders treatments
2016 - Elsevier BV | Urology
Haifeng Lu, Zhigang Ren, Ang Li, Hua Zhang, Jianwen Jiang, Shaoyan Xu, Qixia Luo, Kai Zhou, Xiaoli Sun, Shusen Zheng, Lanjuan Li,
... LC patients. Linear discriminant analysis (LDA) effect size (LEfSe) reveals significant microbial dysbiosis of tongue coats in ... Fusobacterium could distinguish LC patients from healthy subjects. LEfSe outputs show microbial gene functions related to categories ...
Tópico(s): Oral microbiology and periodontitis research
2016 - Nature Portfolio | Scientific Reports
Peng Wu, Chen Yang, Jie Zhao, Guihao Zhang, Jiawei Chen, Junpeng Wang, Huijian Zhang,
... Illumina MiSeq. Sequencing reads were processed using QIIME. LEfSe revealed significant differences in bacterial genera between controls ... distance metric, R = 0.064, P = 0.037). LEfSe demonstrated that 7 genera were increased (e.g., ...
Tópico(s): Urinary Bladder and Prostate Research
2017 - Frontiers Media | Frontiers in Cellular and Infection Microbiology
Yanan Jiao, Zhenchao Zhou, Tao Chen, Yuanyuan Wei, Zheng Ji, Ruixia Gao, Hong Chen,
... throughput qPCR. Linear discriminant analysis (LDA) effect size (LEfSe) was used to discover the differential ARGs (biomarkers) ... distributions of ARGs during seasonal changes and that LEfSe is an acute and effective method for finding ...
Tópico(s): Gut microbiota and health
2017 - Elsevier BV | Environmental Pollution
Shoukun Ji, Hongtao Zhang, Hui Yan, Arash Azarfar, Haitao Shi, Gibson Maswayi Alugongo, Shengli Li, Zhijun Cao, Yajing Wang,
... fractions of rumen content using Venn diagram and LEfSe analysis. Fifteen out of 16 detected biomarkers (using LEfSe analysis) were found in liquid fraction, and these ...
Tópico(s): Genetic and phenotypic traits in livestock
2017 - BioMed Central | Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology
Shaoqing Zhang, Zhongbo Zhou, Yi Li, Fangang Meng,
... study, the linear discriminant analysis (LDA) effect size (LEfSe) algorithm was used to identify active biomarkers, determining ... determining the microbial community structure. More importantly, the LEfSe algorithm and network analysis showed that most of ...
Tópico(s): Membrane Separation Technologies
2017 - Elsevier BV | Chemosphere
Aafke W. F. Janssen, Tom Houben, Saeed Katiraei, Wieneke Dijk, Lily Boutens, Nieke van der Bolt, Zeneng Wang, J. Mark Brown, Stanley L. Hazen, Stéphane Mandard, Ronit Shiri‐Sverdlov, Folkert Kuipers, Ko Willems van Dijk, Jacques Vervoort, Rinke Stienstra, Guido Hooiveld, Sander Kersten,
... used the linear discriminant analysis (LDA) effect size (LEfSe) method (https://bitbucket.org/biobakery/biobakery/wiki/lefse) (36Segata N. Izard J. Waldron L. Gevers D. ...
Tópico(s): Diet and metabolism studies
2017 - Elsevier BV | Journal of Lipid Research
Melody Smith, Eric R. Littmann, John Slingerland, Annelie Clurman, Ann E. Slingerland, Ying Taur, Jonas Schlüter, Jae H. Park, Roisin E. O’Cearbhaill, Sham Mailankody, Eric L. Smith, Maria Lia Palomba, Oladapo O. Yeku, Jonathan U. Peled, Elizabeth Halton, Claudia Diamonte, Jason Chan, Malloury Hall, Pavan Anant, Peter E. Kane, Sergio Giralt, Isabelle Rivière, Renier J. Brentjens, Eric G. Pamer, Marcel R.M. van den Brink,
... to 4 neurotoxicity. Linear discriminant analysis effect size (LEfSe) was used to identify microbial biomarkers for efficacy ... of the efficacy of CAR T cells with LEfSe analysis found increased abundance in several families of ...
Tópico(s): Cancer Immunotherapy and Biomarkers
2018 - Elsevier BV | Blood
Annamaria Painold, Sabrina Mörkl, Karl Kashofer, Bettina Halwachs, Nina Dalkner, Susanne Bengesser, Armin Birner, Frederike T. Fellendorf, Martina Platzer, Robert Queissner, Gregor Schütze, Markus Schwarz, Natalie Moll, Peter Holzer, Anna K. Holl, H.P. Kapfhammer, Gregor Gorkiewicz, Eva Z. Reininghaus,
... of taxa encompassed linear discriminant analysis effect size (LEfSe).We found a negative correlation between microbial alpha- ... anthropometrics and metabolic syndrome in individuals with BD. LEfSe identified the phylum Actinobacteria (LDA= 4.82, P = ...
Tópico(s): Tryptophan and brain disorders
2018 - Wiley | Bipolar Disorders
Gloria Solano‐Aguilar, Saebyeol Jang, Sukla Lakshman, Richi Gupta, Ethiopia Beshah, Masoumeh Sikaroodi, Bryan T. Vinyard, Aleksey Molokin, Patrick M. Gillevet, Joseph F. Urban,
... taxonomic analysis and linear discriminant analysis effect size (LEfSe) to determine bacterial abundance and metabolic function. Pigs ... LPS-stimulated PBMC or the intestinal mucosa transcriptome. LEfSe indicated increases in Lachnospiraceae, Ruminococcaceae within the order ...
Tópico(s): Pharmacological Effects of Natural Compounds
2018 - Multidisciplinary Digital Publishing Institute | Nutrients
Corrie M. Whisner, Juan Maldonado, Brandon Dente, Rosa Krajmalnik‐Brown, Meg Bruening,
... physical activity and fiber intake using QIIME and LEfSe bioinformatics software.No statistically significant differences were observed ... 0, 315.0) min/d. Microbial analysis by LEfSe identified Paraprevotellaceae, Lachnospiraceae, and Lachnospira as important phylotypes ...
Tópico(s): Obesity, Physical Activity, Diet
2018 - BioMed Central | BMC Microbiology
Yanrong Lv, Xiangxiang Qin, Huaijie Jia, Chen Si-rui, Weiwei Sun, Xiaoxia Wang,
... conducted by linear discriminant analysis (LDA) effect size (LEfSe). NGS revealed that gut microbiota composition was different ... diversity decreased with the increase in BMI. And LEfSe analysis indicated that Blautia , Anaerotruncus and its uncultured ...
Tópico(s): Dietary Effects on Health
2019 - Cambridge University Press | British Journal Of Nutrition
Alessandra Lo Presti, Francesca Zorzi, Federica Del Chierico, Annamaria Altomare, Silvia Cocca, Alessandra Avola, Fabiola De Biasio, Alessandra Russo, Eleonora Cella, Sofia Reddel, Emma Calabrese, Livia Biancone, Giovanni Monteleone, Michele Cicala, Silvia Angeletti, Massimo Ciccozzi, Lorenza Putignani, Michele Pier Luca Guarino,
... mucosal microbiota analysis. Linear discriminant analysis effect size (LEfSe) was used for biomarker discovery associated to IBD ... inflamed and not inflamed mucosa. Based upon the LEfSe data, the Anaerostipes and Ruminococcaceae were identified as ...
Tópico(s): Clostridium difficile and Clostridium perfringens research
2019 - Frontiers Media | Frontiers in Microbiology
Fei Zhang, Yue Li, Xiliang Wang, Sheng-Ping Wang, Dingren Bi,
... identified using a linear discriminant and effect size (LEfSe) analysis. Aliihoeflea was established to be the genus ... bacteria in the intestine. Moreover, according to the LEfSe analysis, the DSS group was impacted more significantly ...
Tópico(s): Clostridium difficile and Clostridium perfringens research
2019 - Hindawi Publishing Corporation | BioMed Research International
Kyrill Schoilew, Helena Ueffing, Alexander H. Dalpke, Björn Wolff, Cornelia Frese, Diana Wolff, Sébastien Boutin,
... to patients with previous caries. LDA effect size (LEfSe) analysis demonstrated that the genus Haemophilus is significantly ... caries experience. For the group without caries experience LefSe analysis showed a set of 11 genera being ...
Tópico(s): Gut microbiota and health
2019 - Taylor & Francis | Journal of Oral Microbiology
Jasmohan S. Bajaj, Andrew Fagan, Edith Gavis, Zain Kassam, Masoumeh Sikaroodi, Patrick M. Gillevet,
... Principal component and linear discriminant analysis effect size (LEFSe) analyses were performed. All participants were receiving lactulose, ... the FMT arm long term (Figure 1F) on LEFSe. Lachnospiraceae and Ruminococcaceae species relative abundance remained similar ...
Tópico(s): Gastrointestinal motility and disorders
2019 - Elsevier BV | Gastroenterology
Guangtian Cao, Tingting Song, Yingyue Shen, Qunli Jin, Weilin Feng, Lijun Fan, Weiming Cai,
... families by linear discriminant analysis with effect size (LEfSe) analysis. The analysis of fungal communities showed that ... closer to AF1 in the clustering dendrogram. By LEfSe analysis, Mycothermus thermophilus , Gonapodya polymorpha , and Phaeophleospora_eugeniae ...
Tópico(s): Composting and Vermicomposting Techniques
2019 - American Society for Horticultural Science | HortScience