joda

Joint Deregulation Analysis (JODA). joda is an R package implementing the JODA algorithm introduced in [Szczurek et al.]. The algorithm takes as input perturbation data of the same regulators in two different cell populations, and the information about the cellular context: known transcription factor targets and known topologies of signaling pathway (for both populations). It next proceeds in three steps: (1) Computing probabilities of differential expression of the genes in the perturbation experiments. Here, the known TF targets are used as examples of differential genes. The differential expression analysis is performed using our approach implemented in the bgmm package. The approach performs partially supervised mixture modeling of the perturbation data. (2) Computing regulation scores. For each regulator and each cell population, regulation scores are obtained as an average of the probabilities of differential expression over those perturbation experiments that affect this regulator in this population. (3) Computing deregulation scores. For each regulator deregulation scores are obtained as a difference of the regulation scores for this regulator between the cell populations.

References in zbMATH (referenced in 2 articles )

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  1. Ishan Patel, Blesson Varghese, Adam Barker: RBioCloud: A Light-weight Framework for Bioconductor and R-based Jobs on the Cloud (2014) arXiv
  2. Szczurek, Ewa; Markowetz, Florian; Gat-Viks, Irit; Biecek, Przemyslaw; Tiuryn, Jerzy; Vingron, Martin: Deregulation upon Dna damage revealed by joint analysis of context-specific perturbation data (2011) ioport