Taki, T. | Search bioRxiv

bioRxiv2026

TSUMUGI: a platform for phenotype-driven gene network identification from comprehensive knockout mouse phenotyping data

SummaryDeciphering complex organismal phenotypes requires elucidation of coordinated functions among multiple genes, yet this remains a fundamental challenge in functional genetics. The International Mouse Phenotyping Consortium (IMPC) has recently established a comprehensive phenotypic atlas based on systematic single-gene knockout mouse lines, providing an unprecedented resource for gene-phenotype associations in mammals. However, extracting phenotype-associated multiple gene relationships remains challenging. Here, we present TSUMUGI, a platform that identifies a phenotype-driven gene network by leveraging gene-phenotype associations from the IMPC. TSUMUGI enables users to initiate analyses from a user-specified phenotype or gene list and interactively explore a gene network. In addition, TSUMUGI highlights human disease-associated genes, supports flexible network filtering, and allows seamless export of a gene network for downstream analyses. By linking shared phenotypic signatures to putative functional gene modules, TSUMUGI provides a framework for systematic interpretation and hypothesis generation of complex organismal phenotypes. Availability and implementationThe web application is available online at https://larc-tsukuba.github.io/tsumugi/. The command-line tools are distributed via PyPI (https://pypi.org/project/TSUMUGI) and Bioconda (https://bioconda.github.io/recipes/tsumugi/README.html). Source code and documentation are hosted at GitHub (https://github.com/akikuno/TSUMUGI-dev) and archived on Zenodo (https://doi.org/10.5281/zenodo.18464478) under the MIT license.

bioinformatics↗

bioRxiv2024

KOnezumi-AID: A Software to Automate the Design of Multiplex Knockouts Using Target-AID

With the groundbreaking advancements in genome editing technologies, particularly CRISPR-Cas9, creating knockout mutants has become highly efficient. However, the CRISPR-Cas9 system introduces DNA double-strand breaks, which can increase the risk of chromosomal rear-rangements, presenting a major obstacle when attempting to knockout multiple genes simultaneously. Base editing systems like Target-AID provide a safer alternative by enabling precise base modifications without requiring DNA double-strand breaks, making them a promising solution for addressing this challenge. Nevertheless, the absence of adequate tools to support Target-AID-based gene knockouts highlights the need for a comprehensive system to design guide RNA (gRNA) for the simultaneous knockout of multiple genes. Here, we present KOnezumi-AID, a command-line tool designed to facilitate gRNA design for Target-AID-mediated genome editing. KOnezumi-AID supports gene knockout strategies by inducing premature termination codons or promoting exon skipping. It generates experiment-ready gRNA designs for both mouse and human genomes. Additionally, KOnezumi-AID offers batch processing capabilities, enabling rapid and precise gRNA design for large-scale genome editing projects such as CRISPR screening. In summary, KOnezumi-AID provides an efficient and user-friendly tool for gRNA design, streamlining genome editing workflows and advancing gene knockout research.

bioinformatics↗