R/CascadeData-package.R
CascadeData-package.RdThese are the data from the agressive subject group the from GSE39411 dataset, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39411, Vallat, L., Kemper, C. A., Jung, N., Maumy-Bertrand, M., Bertrand, F., ..., Bahram, S. (2013). Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia. Proceedings of the National Academy of Sciences, 110(2), 459-464, doi:10.1073/pnas.1211130110
5 leukemic CLL B-lymphocyte of aggressive form were stimulated in vitro with an anti-IgM antibody, activating the B-cell receptor (BCR). We analyzed the gene expression at 4 time points (60, 90, 210 and 390 minutes). Each gene expression measurement is performed both in stimulated cells and in control unstimulated cells.
The data were normalized and are ready to use.
These Experimental Data are used as examples by packages such as the Cascade one doi:10.1093/bioinformatics/btt705 in one of its vignettes. The Cascade package is a modeling tool allowing gene selection, reverse engineering, and prediction in Cascade networks.
Data were collected on HG-U133_Plus_2, Affymetrix Human Genome U133 Plus 2.0 Array.
Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2013). Cascade: a R-package to study, predict and simulate the diffusion of a signal through a temporal gene network. Bioinformatics, btt705.
Vallat, L., Kemper, C. A., Jung, N., Maumy-Bertrand, M., Bertrand, F., ... & Bahram, S. (2013). Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia. Proceedings of the National Academy of Sciences, 110(2), 459-464.