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Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data

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Title: Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data
Authors: Altmann, MC
Rinchai, D
Baldwin, N
Toufiq, M
Whalen, E
Garand, M
Kabeer, BSA
Alfaki, M
Presnell, S
Khaenam, P
Benitez, AA
Mougin, F
Thébault, P
Chiche, L
Jourde-Chiche, N
Phillips, JT
Klintmalm, G
O'Garra, A
Berry, M
Bloom, C
Wilkinson, RJ
Graham, CM
Lipman, M
Lertmemongkolchai, G
Bedognetti, D
Thiebaut, R
Kheradmand, F
Mejias, A
Ramilo, O
Palucka, K
Pascual, V
Banchereau, J
Chaussabel, D
Item Type: Journal Article
Abstract: As the capacity for generating large-scale molecular profiling data continues to grow, the ability to extract meaningful biological knowledge from it remains a limitation. Here, we describe the development of a new fixed repertoire of transcriptional modules, BloodGen3, that is designed to serve as a stable reusable framework for the analysis and interpretation of blood transcriptome data. The construction of this repertoire is based on co-clustering patterns observed across sixteen immunological and physiological states encompassing 985 blood transcriptome profiles. Interpretation is supported by customized resources, including module-level analysis workflows, fingerprint grid plot visualizations, interactive web applications and an extensive annotation framework comprising functional profiling reports and reference transcriptional profiles. Taken together, this well-characterized and well-supported transcriptional module repertoire can be employed for the interpretation and benchmarking of blood transcriptome profiles within and across patient cohorts. Blood transcriptome fingerprints for the 16 reference cohorts can be accessed interactively via: https://drinchai.shinyapps.io/BloodGen3Module/.
Issue Date: 19-Jul-2021
Date of Acceptance: 21-Jun-2021
URI: http://hdl.handle.net/10044/1/90762
DOI: 10.1038/s41467-021-24584-w
ISSN: 2041-1723
Publisher: Nature Research
Start Page: 1
End Page: 19
Journal / Book Title: Nature Communications
Volume: 12
Copyright Statement: © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Sponsor/Funder: Wellcome Trust
Wellcome Trust
National Institutes of Health
Funder's Grant Number: 104803/Z/14/Z
Publication Status: Published
Online Publication Date: 2021-07-19
Appears in Collections:Department of Infectious Diseases
National Heart and Lung Institute
Faculty of Medicine

This item is licensed under a Creative Commons License Creative Commons