A2Sign: Agnostic Algorithms for Signatures—a universal method for identifying molecular signatures from transcriptomic datasets prior to cell-type deconvolution

• Published in: Bioinformatics 2022-01, Vol.38 (4), p.1015-1021
• Main Authors: Boldina, Galina, Fogel, Paul, Rocher, Corinne, Bettembourg, Charles, Luta, George, Augé, Franck
• Format: Article
• Language: English
• Subjects: Algorithms; Exome Sequencing; Gene Expression Profiling; RNA-Seq; Transcriptome
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btab773

Abstract Motivation Molecular signatures are critical for inferring the proportions of cell types from bulk transcriptomics data. However, the identification of these signatures is based on a methodology that relies on prior biological knowledge of the cell types being studied. When working with less known biological material, a data-driven approach is required to uncover the underlying classes and generate ad hoc signatures from healthy or pathogenic tissue. Results We present a new approach, A2Sign: Agnostic Algorithms for Signatures, based on a non-negative tensor factorization (NTF) strategy that allows us to identify cell-type-specific molecular signatures, greatly reduce collinearities and also account for inter-individual variability. We propose a global framework that can be applied to uncover molecular signatures for cell-type deconvolution in arbitrary tissues using bulk transcriptome data. We also present two new molecular signatures for deconvolution of up to 16 immune cell types using microarray or RNA-seq data. Availability and implementation All steps of our analysis were implemented in annotated Python notebooks (https://github.com/paulfogel/A2SIGN). To perform NTF, we used the NMTF package, which can be downloaded using Python pip install. Supplementary information Supplementary data are available at Bioinformatics online.