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Mitch: Multi-contrast pathway enrichment for multi-omics and single-cell profiling data

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Version 1 2020-07-01, 19:51
journal contribution
posted on 2024-06-18, 21:27 authored by A Kaspi, Mark ZiemannMark Ziemann
Abstract Background Inference of biological pathway activity via gene set enrichment analysis is frequently used in the interpretation of clinical and other omics data. With the proliferation of new omics profiling approaches and ever-growing size of data sets generated, there is a lack of tools available to perform and visualise gene set enrichments in analyses involving multiple contrasts. Results To address this, we developed mitch, an R package for multi-contrast gene set enrichment analysis. It uses a rank-MANOVA statistical approach to identify sets of genes that exhibit joint enrichment across multiple contrasts. Its unique visualisation features enable the exploration of enrichments in up to 20 contrasts. We demonstrate the utility of mitch with case studies spanning multi-contrast RNA expression profiling, integrative multi-omics, tool benchmarking and single-cell RNA sequencing. Using simulated data we show that mitch has similar accuracy to state of the art tools for single-contrast enrichment analysis, and superior accuracy in identifying multi-contrast enrichments. Conclusion mitch is a versatile tool for rapidly and accurately identifying and visualising gene set enrichments in multi-contrast omics data. Mitch is available from Bioconductor (https://bioconductor.org/packages/mitch).

History

Journal

BMC Genomics

Volume

21

Article number

447

Pagination

1 - 17

Location

England

Open access

  • Yes

ISSN

1471-2164

eISSN

1471-2164

Language

English

Publication classification

C1 Refereed article in a scholarly journal, C Journal article

Issue

1

Publisher

BMC