TEMPO

TEMPO (TEmporal Modeling of Pathway Outliers)

About

TEMPO is a method for modeling and detecting gene sets with disruption of some temporal pattern of expression.

Given a predefined set of genes S, TEMPO determines if (1) there exists a normal, age related pattern of expression amongst those genes using partial least squares regression, and (2) if that pattern breaks down or is otherwise disrupted under the condition being studied.

If you use TEMPO, please cite:

Pietras, Christopher Michael, Faith Ocitti, and Donna K. Slonim. " TEMPO: Detecting Pathway-Specific Temporal Dysregulation of Gene Expression in Disease." Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. ACM, 2018.

Source Code

TEMPO is available on CRAN.
A script version of TEMPO version 1.0.3, which was used to generate the ACM-BCB 2018 results, is also available. An older version of the tempoR package can replicate these exact results, available here

Results

Results for all four data sets from Tempo Version 1.0.4 (bioRxiv) are available here. Results for all four data sets from the ACM-BCB 2018 submission are available here.