Bioinformatics Seminars

Bioinformatics Seminar

Time: 10:45am Tuesdays.
Venue:
Level 7 Seminar Room 2, WEHI1

15 May 2018

Context-specific functional analysis of systems in cancer

Dharmesh Bhuva
WEHI Bioinformatics

Most current approaches that analyse transcriptional co-expression through network inference focus on a single condition (e.g. disease), motivated by the assumption that co-expression networks are context-specific and therefore vary across conditions. I have been investigating the comparative analysis of co-expression networks across conditions (e.g. disease vs normal), as differences between these conditions may provide better insight into the functional behaviour of a biological system, similar in principle to a differential expression analysis. A range of methods have been proposed for the inference and identification of differentially co-expressed genes, however their applications have been limited as there is no consistent framework for benchmarking and evaluating different methods. Difficulties include incomplete data and missing prior knowledge (i.e. no "perfect" gold-standard network), thus I have developed a simulation-based framework to evaluate the performance of 12 inference methods in the context of regulatory networks. I will discuss how previous evaluations may have underestimated the performance of inference methods due to the metrics applied and gold-standard networks used, and explore some of the network features which are associated with the ability of different inference methods to recapitulate underlying network structure.


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