Gene expression signatures predict circadian rhythms in oncogenic pathways
Winkler, E.; Ananthasubramaniam, B.; Herzel, H.
Show abstract
Day-night environmental cycles together with our own adaptive rhythms in behavior and physiology lead to rhythmicity of various processes on the cellular level, including cell signaling. Despite many implications of such daily changes in signaling, the quantification of such rhythms and estimates of peak phases of pathway activities in various tissues are missing. Governed mainly by posttranslational modifications, a pathway activity might not be well quantified via the expression level of pathway components. Instead, a gene expression signatures approach can be used to score activity of various pathways. Here, we apply such gene expression signatures on circadian time series transcriptomics data to infer rhythmicity in cellular signaling. We show that, across multiple datasets, the gene expression signatures predict the presence of rhythmicity in EGFR, PI3K and p53 pathways in mouse liver. With the focus on EGFR pathway, we pinpoint the most influential signature genes for the overall rhythmicity in the activity scores for this pathway. These findings suggest that time of the day is an important factor to consider in studies on signaling. Simultaneously, this study provides a new paradigm to use circadian transcriptomics to get at temporal dynamics of pathway activation.
Matching journals
The top 7 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- A repeatedly evolved mutation in Cryptochrome-1 of subterranean animals alters behavioral and molecular circadian rhythms 93%
- Nanopore sequencing unveils the complexity of the cold-activated murine brown adipose tissue transcriptome 92%
- Multi-omics analysis identifies essential regulators of mitochondrial stress response in two wild-type C. elegans strains 92%
Similar papers in this journal
- Genome-wide correlation analysis reveals Rorc as potential amplitude regulator of circadian transcriptome output 95%
- Artificial light at night leads to circadian disruption in a songbird: integrated evidence from behavioural, genomic and metabolomic data 93%
- Tuning of liver circadian transcriptome rhythms by thyroid hormone state in male mice 93%
Similar papers in this journal
- Model integration of circadian and sleep-wake driven contributions to rhythmic gene expression reveals novel regulatory principles 93%
- Deciphering the Signaling Network Landscape of Breast Cancer Improves Drug Sensitivity Prediction 91%
- TRIAGE: A web-based iterative analysis platform integrating pathway and network approaches optimizes hit selection from high- throughput assays. 91%
Similar papers in this journal
- The sleep-wake distribution contributes to the peripheral rhythms in PERIOD-2 93%
- The microbiome interacts with the circadian clock and dietary composition to regulate metabolite cycling in the Drosophila gut 92%
- Gene Expression and Tracer-Based Metabolic Flux Analysis Reveals Tissue-Specific Metabolic Scaling in vitro, ex vivo, and in vivo 92%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.