| Type: | Package |
| Title: | Experimental Data of Cascade Experiments in Genomics |
| Version: | 1.5 |
| Date: | 2025-08-21 |
| Depends: | R (≥ 2.10) |
| Suggests: | testthat (≥ 3.0.0) |
| Author: | Frederic Bertrand 
[cre, aut],
Myriam Maumy-Bertrand
[aut],
Laurent Vallat [ctb],
Nicolas Jung [ctb] |
| Maintainer: | Frederic Bertrand <frederic.bertrand@utt.fr> |
| Description: | These experimental expression data (5 leukemic 'CLL' B-lymphocyte of aggressive form from 'GSE39411', <doi:10.1073/pnas.1211130110>), after B-cell receptor stimulation, are used as examples by packages such as the 'Cascade' one, a modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| URL: | https://fbertran.github.io/CascadeData/, https://github.com/fbertran/CascadeData/ |
| BugReports: | https://github.com/fbertran/CascadeData/issues/ |
| Config/testthat/edition: | 3 |
| NeedsCompilation: | no |
| Packaged: | 2025-08-21 23:55:30 UTC; bertran7 |
| Repository: | CRAN |
| Date/Publication: | 2025-08-22 00:10:01 UTC |
CascadeData: Experimental Data of Cascade Experiments in Genomics
Description
These experimental expression data (5 leukemic 'CLL' B-lymphocyte of aggressive form from 'GSE39411', doi:10.1073/pnas.1211130110), after B-cell receptor stimulation, are used as examples by packages such as the 'Cascade' one, a modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) doi:10.1093/bioinformatics/btt705.
Author(s)
This package has been written by Frederic Bertrand, Myriam Maumy-Bertrand and Nicolas Jung with biological insights from Laurent Vallat.
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
References
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.
See Also
Useful links:
Report bugs at https://github.com/fbertran/CascadeData/issues/
Stimulated dataset
Description
This is the stimulated data part of the GSE39411 dataset, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39411. Data were normalized and are ready to use.
Format
A data frame with 54613 probesets measured 6 times throught 4 time
points. It features 54613 rows and 24 numeric columns.
Columns are named **exactly** as:
N1_S_T60, N1_S_T90, N1_S_T210, N1_S_T390,
N2_S_T60, N2_S_T90, N2_S_T210, N2_S_T390,
N3_S_T60, N3_S_T90, N3_S_T210, N3_S_T390,
N4_S_T60, N4_S_T90, N4_S_T210, N4_S_T390,
N5_S_T60, N5_S_T90, N5_S_T210, N5_S_T390,
N6_S_T60, N6_S_T90, N6_S_T210, N6_S_T390.
The ordering is strict: for each replicate N1, N2, N3,
N4 , N5, N6 the time points are
ordered T60, T90, T210, T390.
Details
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. This is the stimulated cells dataset.
Data were collected on HG-U133_Plus_2, Affymetrix Human Genome U133 Plus 2.0 Array.
References
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.
Examples
data(micro_S)
Unstimulated control dataset
Description
This is the unstimulated data part of the GSE39411 dataset, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39411. Data were normalized and are ready to use.
Format
A data frame with 54613 probesets measured 6 times throught 4 time
points. It features 54613 rows and 24 numeric columns.
Columns are named **exactly** as:
N1_US_T60, N1_US_T90, N1_US_T210, N1_US_T390,
N2_US_T60, N2_US_T90, N2_US_T210, N2_US_T390,
N3_US_T60, N3_US_T90, N3_US_T210, N3_US_T390,
N4_US_T60, N4_US_T90, N4_US_T210, N4_US_T390,
N5_US_T60, N5_US_T90, N5_US_T210, N5_US_T390,
N6_US_T60, N6_US_T90, N6_US_T210, N6_US_T390.
The ordering is strict: for each replicate N1, N2, N3,
N4 , N5, N6 the time points are
ordered T60, T90, T210, T390.
A data frame with 54613 probesets measured 6 times throught 4 time points.
Details
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. This is the unstimulated cells dataset.
Data were collected on HG-U133_Plus_2, Affymetrix Human Genome U133 Plus 2.0 Array.
References
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.
Examples
data(micro_US)