Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage
Daniel Carbajo, Shigeyuki Magi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Erik Arner, Alistair RR Forrest, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub, Mariko Okada-Hatakeyama, Jessica C Mar
PLoS One | PUBLIC LIBRARY SCIENCE | Published : 2015
Understanding how cells use complex transcriptional programs to alter their fate in response to specific stimuli is an important question in biology. For the MCF-7 human breast cancer cell line, we applied gene expression trajectory models to identify the genes involved in driving cell fate transitions. We modified trajectory models to account for the scenario where cells were exposed to different stimuli, in this case epidermal growth factor and heregulin, to arrive at different cell fates, i.e. proliferation and differentiation respectively. Using genome-wide CAGE time series data collected from the FANTOM5 consortium, we identified the sets of promoters that were involved in the transitio..View full abstract
Awarded by Grants-in-Aid for Scientific Research
FANTOM5 was made possible by the following grants: Research Grant for RIKEN Omics Science Center from MEXT to YH; Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to YH; Research Grant from MEXT to the RIKEN Center for Life Science Technologies; Research Grant to RIKEN Preventive Medicine and Diagnosis Innovation Program from MEXT to YH.