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

Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data. Altman, M. C, Rinchai, D., Baldwin, N., Toufiq, M., Whalen, E., Garand, M., Syed Ahamed Kabeer, B., Alfaki, M., Presnell, S. R, Khaenam, P., Ayllón-Benítez, A., Mougin, F., Thébault, P., Chiche, L., Jourde-Chiche, N., Phillips, J T., Klintmalm, G., O'Garra, A., Berry, M., Bloom, C., Wilkinson, R. J, Graham, C. M, Lipman, M., Lertmemongkolchai, G., Bedognetti, D., Thiebaut, R., Kheradmand, F., Mejias, A., Ramilo, O., Palucka, K., Pascual, V., Banchereau, J., & Chaussabel, D. Nature Communications, 12(1):4385, Nature Publishing Group, dec, 2021.

Paper doi abstract bibtex

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/ .

@article{Altman2021,
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/ .},
author = {Altman, Matthew C and Rinchai, Darawan and Baldwin, Nicole and Toufiq, Mohammed and Whalen, Elizabeth and Garand, Mathieu and {Syed Ahamed Kabeer}, Basirudeen and Alfaki, Mohamed and Presnell, Scott R and Khaenam, Prasong and Ayll{\'{o}}n-Ben{\'{i}}tez, Aaron and Mougin, Fleur and Th{\'{e}}bault, Patricia and Chiche, Laurent and Jourde-Chiche, Noemie and Phillips, J Theodore and Klintmalm, Goran and O'Garra, Anne and Berry, Matthew and Bloom, Chloe and Wilkinson, Robert J and Graham, Christine M and Lipman, Marc and Lertmemongkolchai, Ganjana and Bedognetti, Davide and Thiebaut, Rodolphe and Kheradmand, Farrah and Mejias, Asuncion and Ramilo, Octavio and Palucka, Karolina and Pascual, Virginia and Banchereau, Jacques and Chaussabel, Damien},
doi = {10.1038/s41467-021-24584-w},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Altman et al. - 2021 - Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data.pdf:pdf},
issn = {2041-1723},
journal = {Nature Communications},
keywords = {Data mining,OA,Systems biology,Translational immunology,fund{\_}ack,original},
mendeley-tags = {OA,fund{\_}ack,original},
month = {dec},
number = {1},
pages = {4385},
pmid = {34282143},
publisher = {Nature Publishing Group},
title = {{Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data}},
url = {https://www.nature.com/articles/s41467-021-24584-w http://www.nature.com/articles/s41467-021-24584-w},
volume = {12},
year = {2021}
}

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