Himori, K. | Search bioRxiv

bioRxiv2024

HuTAge: a Comprehensive Human Tissue- and Cell-specific Ageing Signature Atlas

SummaryAgeing is a complex process that involves interorgan and intercellular interactions. To obtain a clear understanding of ageing, cross-tissue single-cell data resources are required. However, a complete resource for humans is not available. To bridge this gap, we developed HuTAge, a comprehensive resource that integrates cross-tissue age-related information from The Genotype-Tissue Expression project with cross-tissue single-cell information from Tabula Sapiens to provide human tissue- and cell-specific ageing molecular information. Availability and ImplementationHuTAge is implemented within an R Shiny application and can be freely accessed at https://igcore.cloud/GerOmics/HuTAge/home. The source code is available at https://github.com/matsui-lab/HuTAge. Contacthimori.koichi.b5@f.mail.nagoya-u.ac.jp

bioinformatics↗

bioRxiv2024

A Computational Approach to Interpreting the Embedding Space of Dimension Reduction

Nonlinear dimension reduction methods are widely applied in studies analyzing gene and protein expression, by revealing patterns of discrete groups and continuous orders in high-dimensional data. However, the tools are limited to understanding the obtained embedding structures of biological mechanisms, hindering the full exploitation of data. Here, we propose a novel framework to interpret embedding systematically by identifying and mapping associated biological functions. The method performs statistical tests and visualizes significantly enriched functions essential for the organization of the embedding structure, by applying it to the embedding results of two datasets: the Genotype Tissue Expression dataset and a Caenorhabditis elegans embryogenesis dataset, one capturing distinct cluster structures and the other capturing continuous developmental trajectories. We identified the associated functions for interpreting the two embeddings and confirmed it as a useful explainable AI tool in exploratory data analysis by providing annotations to the embedding space.

bioinformatics↗