Examining microbe-metabolite correlations by linear methods.

作者: Thomas P. Quinn , Ionas Erb

DOI: 10.1038/S41592-020-01006-1

关键词: General partnershipLinear methodsWelfare economicsHorizon (archaeology)Political scienceChristian ministryEuropean Regional Development FundEuropean union

摘要: Funding: I.E. has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No. 825835 (BovReg), Secretaria de Universidades e Investigacion del Departamento Economia y Conocimiento la Generalidad Cataluna, 2017 SGR 447 (SGR), Agencia Estatal (AEI) FEDER Project BFU2017-88264-P (Plan Estatal). also acknowledges following CRG sources: support of Spanish Ministry Economy, Industry Competitiveness (MEIC) to EMBL partnership, Centro Excelencia Severo Ochoa, CERCA / Generalitat Catalunya Regional Development Fund (ERDF)

参考文章(14)
Zachary D. Kurtz, Christian L. Müller, Emily R. Miraldi, Dan R. Littman, Martin J. Blaser, Richard A. Bonneau, Sparse and Compositionally Robust Inference of Microbial Ecological Networks PLOS Computational Biology. ,vol. 11, pp. e1004226- 25 ,(2015) , 10.1371/JOURNAL.PCBI.1004226
Javier Palarea-Albaladejo, Josep Antoni Martín-Fernández, zCompositions — R package for multivariate imputation of left-censored data under a compositional approach Chemometrics and Intelligent Laboratory Systems. ,vol. 143, pp. 85- 96 ,(2015) , 10.1016/J.CHEMOLAB.2015.02.019
David Lovell, Vera Pawlowsky-Glahn, Juan José Egozcue, Samuel Marguerat, Jürg Bähler, Proportionality: A Valid Alternative to Correlation for Relative Data PLOS Computational Biology. ,vol. 11, pp. e1004075- 12 ,(2015) , 10.1371/JOURNAL.PCBI.1004075
Andrew D Fernandes, Jennifer NS Reid, Jean M Macklaim, Thomas A McMurrough, David R Edgell, Gregory B Gloor, Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis Microbiome. ,vol. 2, pp. 15- 15 ,(2014) , 10.1186/2049-2618-2-15
Ionas Erb, Cedric Notredame, How should we measure proportionality on relative gene expression data? Theory in Biosciences. ,vol. 135, pp. 21- 36 ,(2016) , 10.1007/S12064-015-0220-8
Cameron Martino, James T. Morton, Clarisse A. Marotz, Luke R. Thompson, Anupriya Tripathi, Rob Knight, Karsten Zengler, A Novel Sparse Compositional Technique Reveals Microbial Perturbations. mSystems. ,vol. 4, ,(2019) , 10.1128/MSYSTEMS.00016-19
Tang ZhengZheng Tang ZhengZheng, Chen GuanHua Chen GuanHua, Hong QiLin Hong QiLin, Huang Shi Huang Shi, HM Smith, RD Shah, M Scholz, JF Ferguson, Multi-Omic Analysis of the Microbiome and Metabolome in Healthy Subjects Reveals Microbiome-Dependent Relationships Between Diet and Metabolites Frontiers in Genetics. ,vol. 10, pp. 454- 454 ,(2019) , 10.3389/FGENE.2019.00454
Jason Lloyd-Price, Cesar Arze, Ashwin N Ananthakrishnan, Melanie Schirmer, Julian Avila-Pacheco, Tiffany W Poon, Elizabeth Andrews, Nadim J Ajami, Kevin S Bonham, Colin J Brislawn, David Casero, Holly Courtney, Antonio Gonzalez, Thomas G Graeber, A Brantley Hall, Kathleen Lake, Carol J Landers, Himel Mallick, Damian R Plichta, Mahadev Prasad, Gholamali Rahnavard, Jenny Sauk, Dmitry Shungin, Yoshiki Vázquez-Baeza, Richard A White III, Jonathan Braun, Lee A Denson, Janet K Jansson, Rob Knight, Subra Kugathasan, Dermot PB McGovern, Joseph F Petrosino, Thaddeus S Stappenbeck, Harland S Winter, Clary B Clish, Eric A Franzosa, Hera Vlamakis, Ramnik J Xavier, Curtis Huttenhower, None, Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. ,vol. 569, pp. 655- 662 ,(2019) , 10.1038/S41586-019-1237-9
Shinichi Yachida, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Takeshi Nakajima, Taku Sakamoto, Hikaru Watanabe, Keigo Masuda, Yuichiro Nishimoto, Masaru Kubo, Fumie Hosoda, Hirofumi Rokutan, Minori Matsumoto, Hiroyuki Takamaru, Masayoshi Yamada, Takahisa Matsuda, Motoki Iwasaki, Taiki Yamaji, Tatsuo Yachida, Tomoyoshi Soga, Ken Kurokawa, Atsushi Toyoda, Yoshitoshi Ogura, Tetsuya Hayashi, Masanori Hatakeyama, Hitoshi Nakagama, Yutaka Saito, Shinji Fukuda, Tatsuhiro Shibata, Takuji Yamada, Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer Nature Medicine. ,vol. 25, pp. 968- 976 ,(2019) , 10.1038/S41591-019-0458-7