TRanscriptome ANalysis of StratifiEd CohorTs (TRANSECT) enables automated assessment of global gene regulation linked to disparate expression in user defined genes and gene sets
Publicly accessible expression data produced by large consortium projects like TCGA and GTEx are increasing in number and size at an unprecedented rate. Their utility cannot be underestimated given the diversity of valuable tools widely used to interrogate these data and the many discoveries of biological and clinical significance already garnered from these datasets. However, there remain undiscovered ways to mine these rich resources and a continuing need to provide researchers with easily accessible and user-friendly applications for complex or bespoke analyses. We introduce TRanscriptome ANalysis of StratifiEd CohorTs (TRANSECT), a bioinformatics application automating the stratification and subsequent differential expression analysis of cohort data to provide further insights into gene regulation. TRANSECT works by defining two groups within a cohort based on disparate expression of a gene or a gene set and subsequently compares the groups for differences in global expression. Akin to reverse genetics minus the inherent requirement of <i>in vitro</i> or <i>in vivo</i> perturbations, cell lines or model organisms and all the while working within natural physiological limits of expression, TRANSECT compiles information about global transcriptomic change and functional outcomes. TRANSECT is freely available as a command line application or online at https://transect.au.
Authors
- Susan Branford (ORCID: https://orcid.org/0000-0002-5095-7981)
- Luke A. Selth (ORCID: https://orcid.org/0000-0002-4686-1418)
- Nicholas I. Warnock (ORCID: https://orcid.org/0000-0003-3422-3184)
- Angel F. López (ORCID: https://orcid.org/0000-0001-7430-0135)
- Hamish S. Scott (ORCID: https://orcid.org/0000-0002-5813-631X)
- David M. Lawrence (ORCID: https://orcid.org/0000-0002-2968-3023)
- Chung Hoow Kok (ORCID: https://orcid.org/0000-0002-3181-7852)
- Cameron P. Bracken (ORCID: https://orcid.org/0000-0001-7722-625X)
- Simon J. Conn (ORCID: https://orcid.org/0000-0002-1376-4515)
- Gregory J. Goodall (ORCID: https://orcid.org/0000-0003-1294-0692)
- Winnie L. Kan (ORCID: https://orcid.org/0000-0002-5844-7644)
- John Toubia (ORCID: https://orcid.org/0000-0002-5135-6504)
- Philip A. Gregory (ORCID: https://orcid.org/0000-0002-0999-0632)
- Andreas Schreiber (ORCID: https://orcid.org/0000-0002-9081-3405)
- Muneeza Maqsood
- Yasir Kusay (ORCID: https://orcid.org/0009-0000-2777-2631)
Institutions
- South Australia Pathology (AU)
- Flinders University (AU)
- University of South Australia (AU)
- Centre for Cancer Biology (AU)
- Freemasons Foundation Centre for Men's Health (AU)
- The University of Adelaide (AU)
Publication Details
- Journal
- NAR Genomics and Bioinformatics
- Published
- 2025-03-29
- DOI
- https://doi.org/10.1093/nargab/lqaf041
- Primary Topic
- Bioinformatics and Genomic Networks
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Hospital Research Foundation
- Australian Government
- Australian Cancer Research Foundation
- National Breast Cancer Foundation
- Therapeutic Innovation Australia
- Australian Research Data Commons
- Tour de Cure
- Medical Research Council
- National Health and Medical Research Council
- Cancer Council South Australia
- Royal Adelaide Hospital Research Fund