Journal article

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

Dharmesh D Bhuva, Joseph Cursons, Gordon K Smyth, Melissa J Davis

Genome Biology | BMC | Published : 2019

Abstract

BACKGROUND: Elucidation of regulatory networks, including identification of regulatory mechanisms specific to a given biological context, is a key aim in systems biology. This has motivated the move from co-expression to differential co-expression analysis and numerous methods have been developed subsequently to address this task; however, evaluation of methods and interpretation of the resulting networks has been hindered by the lack of known context-specific regulatory interactions. RESULTS: In this study, we develop a simulator based on dynamical systems modelling capable of simulating differential co-expression patterns. With the simulator and an evaluation framework, we benchmark and ch..

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Grants

Awarded by National Health and Medical Research Council


Awarded by NBCF Career Development Fellowship


Funding Acknowledgements

This work was supported by National Health and Medical Research Council funding (Project Grant 1128609 to MJD, Project Grant 1147528 to JC, Fellowship 1154970 to GKS). MJD was supported by NBCF Career Development Fellowship ECF-14-043 and is the recipient of the Betty Smyth Centenary Fellowship in Bioinformatics. DDB was supported by the Melbourne Research Scholarship (MRS). This study was made possible through Victorian State Government Operational Infrastructure Support and Australian Government NHMRC Independent Research Institute Infrastructure Support scheme.