Title

MASHt: Software for statistical analysis of transcriptomes' qualitative features in factorial experiments

Authors

Maria Nuc¹, Michał Stanoch¹, Hanna Ćwiek-Kupczyńska^1,2, Barbara Naganowska¹ & Paweł Krajewski^1,*

Affiliation

¹Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland; ²Luxembourg Centre for Systems Biomedicine, University du Luxembourg, 1 Bd du Jazz, 4370 Esch-Belval, Luxembourg ; *Corresponding author

Email

Maria Nuc - E-mail: mnuc@igr.poznan.pl
Michał Stanoch - E-mail: msta@igr.poznan.pl
Hanna Ćwiek-Kupczyńska - E-mail: hanna@cwiek-kupczynska.com

Barbara Naganowska - E-mail: bnag@igr.poznan.pl
Paweł Krajewski - E-mail: pkra@igr.poznan.pl

Article Type

Research Article

Date

Received September 1, 2025; Revised September 30, 2025; Accepted September 30, 2025, Published September 30, 2025

Abstract

In Next-Generation Sequencing (NGS) data analysis, attention is given more often to the variation in gene expression levels in several experimental variants than to the qualitative differences between transcriptomes. We present the MASHt toolkit for analyzing qualitative variation in sequencing data from multifactorial experiments. The analysis involves computing pairwise Mash distances between datasets, conducting principal coordinate analysis of the resulting distance matrix, and applying univariate and multivariate analyses of variance to the principal coordinates. MASHt supports computations on data subsets, such as those annotated by a specific ontology. We demonstrate the use of MASHt with an example experiment examining the impact of temperature on the transcriptomes of different barley genotypes.

Keywords

Transcriptomics, factorial experiments, sequence variation, software tools

Citation

Nuc et al. Bioinformation 21(9): 3162-3164 (2025)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.