TransSynW
Ribeiro MM, Okawa S, Del Sol A
2020 · Stem cells translational medicine
Generation of desired cell types by cell conversion remains a challenge.
Abstract
From the original paper, Stem cells translational medicine · PubMed
Generation of desired cell types by cell conversion remains a challenge. In particular, derivation of novel cell subtypes identified by single-cell technologies will open up new strategies for cell therapies. The recent increase in the generation of single-cell RNA-sequencing (scRNA-seq) data and the concomitant increase in the interest expressed by researchers in generating a wide range of functional cells prompted us to develop a computational tool for tackling this challenge. Here we introduce a web application, TransSynW, which uses scRNA-seq data for predicting cell conversion transcription factors (TFs) for user-specified cell populations. TransSynW prioritizes pioneer factors among predicted conversion TFs to facilitate chromatin opening often required for cell conversion. In addition, it predicts marker genes for assessing the performance of cell conversion experiments. Furthermore, TransSynW does not require users' knowledge of computer programming and computational resources. We applied TransSynW to different levels of cell conversion specificity, which recapitulated known conversion TFs at each level. We foresee that TransSynW will be a valuable tool for guiding experimentalists to design novel protocols for cell conversion in stem cell research and regenerative medicine.
Summary
Editorial summary pending review by the maintainer. The paper's own abstract appears above; the Atlas summary in the maintainer's voice will explain how TransSynW relates to the cross-modality inverse-design framework of the review.
Why this level
Level 0 because the method scores features against a target/background contrast without modelling an intervention — the output is a ranked list of candidate identity determinants, not an intervention whose effect has been computed. Representation family is signature / state-matching. Cited in §3.1 of the review. Editorial rationale pending review by the maintainer.