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Data-driven approaches towards studying context-specific cell signalling

April 21, 2021, 13:15 - 14:00
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Organizer

Rui Benfeitas, SciLifeLab/Stockholm University
rui.benfeitas@scilifelab.se
Virtual Event Virtual Event
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Data-driven approaches towards studying context-specific cell signalling

Virtual Event Virtual Event

April 21 @ 13:15 14:00 CEST

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Evangelia Petsalaki, Group Leader EMBL/EBI, United Kingdom

When: April 21, 13:15

Zoom: https://stockholmuniversity.zoom.us/j/68215564760

Host: Rui Benfeitas, Stockholm University

Abstract

Our group aims to understand and describe the organisation principles of cell signalling that allow the diverse and context-specific cell responses and phenotypes.It is well established that signalling responses happen through complex networks. However, most signalling research still uses linear pathways as the ground truth. Moreover, signalling responses are highly dependent on context, such as tissue type, genetic background etc and therefore these static pathways are not always suitable. There is also a high bias in the literature towards kinases and pathways for which reagents and prior knowledge is readily available. This leaves a huge dark space in our understanding of cell signalling and significantly hinders studies of its general principles.In this talk I will present two projects where we try to mitigate some of the above issues. For the first one I will present CEN-tools, an integrative webserver and python package, that allows users to navigate the contexts of different gene essentialities. I will demonstrate examples of its use in discovering new gene-gene relationships and important putative signalling targets for different cancers. For the second one I will present a method that combines paired transcriptomics and imaging data to extract context-specific signalling networks, with the context in this case cell shape in breast cancer. The method is generalisable to any paired transcriptomics/phenotype data.