| Title: | Example data for the diggit package |
|---|---|
| Description: | This package provides expression profile and CNV data for glioblastoma from TCGA, and transcriptional and post-translational regulatory networks assembled with the ARACNe and MINDy algorithms, respectively. |
| Authors: | Mariano Javier Alvarez |
| Maintainer: | Mariano Javier Alvarez <[email protected]> |
| License: | GPL (>=2) |
| Version: | 1.45.0 |
| Built: | 2026-10-10 10:35:26 UTC |
| Source: | https://github.com/bioc/diggitdata |
This package contains a human glioblastoma mRNA expression dataset, a human glioblastoma copy number variation (CNV) dataset, a glioblastoma context-specific transcriptional network, and a glioblastoma context-specific post-translational network.
| Package: | diggitdata |
| Type: | Package |
| Version: | 0.99.0 |
| Date: | 2014-08-29 |
| License: | GPL (>=2) |
| LazyLoad: | yes |
Mariano Javier Alvarez
Maintainer: Mariano Javier Alvarez <[email protected]>
Human glioblastoma transcriptional regulatory network assembled by the ARACNe algorithm from TCGA expression data. The data is stored in a S3 class 'regulon' object.
data(gbm.aracne)data(gbm.aracne)
Margolin,A.A. et al. (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 7 Suppl 1, S7.
data(gbm.aracne) print(gbmTFregulon)data(gbm.aracne) print(gbmTFregulon)
Normalized CNV data, sumarized at the gene level, for 230 samples from TCGA profiled by Agilent HG-CGH-244A arrays. The CNV data is in a matrix format, with samples in columns and genes in rows.
data(gbm.cnv)data(gbm.cnv)
data(gbm.cnv) print(gbmCNV[1:5, 1:5])data(gbm.cnv) print(gbmCNV[1:5, 1:5])
Normalized CNV data, sumarized at the gene level, for 33 blood samples from TCGA profiled by Agilent HG-CGH-244A arrays. The CNV data is in a matrix format, with samples in columns and genes in rows.
data(gbm.cnv.normal)data(gbm.cnv.normal)
data(gbm.cnv.normal) print(gbmCNVnormal[1:5, 1:5])data(gbm.cnv.normal) print(gbmCNVnormal[1:5, 1:5])
ExpressionSet object containing cleaner summarized and mas5 normalized mRNA expression data from 250 human glioblastoma samples profiled by TCGA on HT-HGU133A arrays.
data(gbm.expression)data(gbm.expression)
Alvarez,M.J. et al. (2009) Correlating measurements across samples improves accuracy of large-scale expression profile experiments. Genome Biol., 10, R143.
data(gbm.expression) print(gbmExprs)data(gbm.expression) print(gbmExprs)
Human glioblastoma post-translational regulatory network assembled by the MINDy algorithm from TCGA expression data. The data is stored in a S3 class 'regulon' object.
data(gbm.mindy)data(gbm.mindy)
Wang,K. et al. (2009) Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat. Biotechnol., 27, 829-39.
data(gbm.mindy) print(gbmMindy)data(gbm.mindy) print(gbmMindy)