Title | Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data. |
Publication Type | Journal Article |
Year of Publication | 2021 |
Authors | Altman MC, Rinchai D, Baldwin N, Toufiq M, Whalen E, Garand M, Kabeer BSyed Ahame, Alfaki M, Presnell SR, Khaenam P, Ayllón-Benítez A, Mougin F, Thébault P, Chiche L, Jourde-Chiche N, J Phillips T, 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 |
Journal | Nat Commun |
Volume | 12 |
Issue | 1 |
Pagination | 4385 |
Date Published | 2021 07 19 |
ISSN | 2041-1723 |
Keywords | Bacteria, Blood, Blood Chemical Analysis, Cluster Analysis, Computational Biology, Gene Expression Profiling, Gene Regulatory Networks, Humans, Transcriptome |
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/ . |
DOI | 10.1038/s41467-021-24584-w |
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Alternate Journal | Nat Commun |
PubMed ID | 34282143 |
PubMed Central ID | PMC8289976 |
Grant List | FC10218 / WT_ / Wellcome Trust / United Kingdom FC10218 / CRUK_ / Cancer Research UK / United Kingdom U01 AI115940 / AI / NIAID NIH HHS / United States U19 AI067854 / AI / NIAID NIH HHS / United States U01 AI082110 / AI / NIAID NIH HHS / United States 203135 / WT_ / Wellcome Trust / United Kingdom U01 AI067854 / AI / NIAID NIH HHS / United States 104803 / WT_ / Wellcome Trust / United Kingdom / WT_ / Wellcome Trust / United Kingdom |