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First published online October 23, 2009
doi: 10.1242/10.1242/dev.030320

Development 136, 3729-3740 (2009)
Published by The Company of Biologists 2009
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Review

Informatics approaches to understanding TGFβ pathway regulation

Pascal Kahlem1 and Stuart J. Newfeld2,3,*

1 EMBL, European Bioinformatics Institute, Hinxton, Saffron Waldon CB10 1SD, UK.
2 School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
3 Center for Evolutionary Functional Genomics, Arizona State University, Tempe, AZ 85287, USA.

* Author for correspondence (newfeld{at}asu.edu)

SUMMARY

In recent years, informatics studies have predicted several new ways in which the transforming growth factor β (TGFβ) signaling pathway can be post-translationally regulated. Subsequently, many of these predictions were experimentally validated. These approaches include phylogenetic predictions for the phosphorylation, sumoylation and ubiquitylation of pathway components, as well as kinetic models of endocytosis, phosphorylation and nucleo-cytoplasmic shuttling. We review these studies and provide a brief `how to' guide for phylogenetics. Our hope is to stimulate experimental tests of informatics-based predictions for TGFβ signaling, as well as for other signaling pathways, and to expand the number of developmental pathways that are being analyzed computationally.


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© The Company of Biologists Ltd 2009