Robust analysis of comparative subcellular omics with complex designs

Authors

Crook, O., Andrejeva, A., Queiroz, R., Smith, T. S., Breckels, L., Lilley, K.

Abstract

Subcellular omics technologies now allow us to obtain insights into steady-state localisation and re-localisation of biomolecules in high-throughput. However, robust analysis of these experiments can be slow and challenging. Here, we show that existing approaches to differential localisation fall into two classes, marker-dependent and marker-free, that fail for fundamentally different statistical reasons, with failure modes that are not completely overlapping. We exploit this observation in SANDLE (statistical analysis of differential localisation experiments), which combines a marker-dependent generative model of subcellular niches with a marker-free regression test for changes in fractionation profiles. This dual strategy provides better control of false positives, up to 100-fold reduction in analysis time, and accommodates more complex experimental designs than existing methods. We demonstrate SANDLE's versatility across a wide range of subcellular omics experiments, including drug-treatment responses, cross-species and life-cycle comparisons, post-translationally modified proteoforms, and RNA re-localisation. Co-analysing transcriptome and proteome dynamics during the unfolded protein response, we further reveal lncRNAs whose steady-state localisation is condition-dependent. By addressing key methodological limitations, SANDLE enables broad applications of subcellular omics from fundamental biology to clinical research.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 09 Jul 2026.

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