| Title: | Drug versus Disease Data |
|---|---|
| Description: | Data package which provides default drug and disease expression profiles for the DvD package. |
| Authors: | C. Pacini |
| Maintainer: | J. Saez-Rodriguez <[email protected]> |
| License: | GPL-3 |
| Version: | 1.48.0 |
| Built: | 2026-10-10 11:06:17 UTC |
| Source: | https://github.com/bioc/DvDdata |
Data package to provide default ranked profiles, clusters and Cytoscape http://www.cytoscape.org/ file format for the DvD package.
| Package: | DvDdata |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2012-05-16 |
| License: | GPL-2 |
| LazyLoad: | yes |
Data loaded automatically in the DvD package.
C. Pacini
Maintainer: Julio [email protected]
Drug Profiles: http://www.broadinstitute.org/cmap/ Disease Profiles: http://www.ncbi.nlm.nih.gov/geo/
#load the disease Ranked lists: data(diseaseRL)#load the disease Ranked lists: data(diseaseRL)
Maps the annotation of Affymetrix platforms from the affy [1] package to the annotation names in BioMaRt [2]
data(annotationlist)data(annotationlist)
Matrix 3 rows, 2 columns.
Provided for three Affymetrix platforms HG-U133A, HG-U133A2 and HG-U133Plus2.
[1]Irizarry et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Research, 31(4); e15.
[2]Durinck et al. (2009). Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nature Protocols 4, 1184-1191.
data(annotationlist)data(annotationlist)
Data frame containing information for generating the Cytoscape SIF file. Contains the connections between the affinity propagation clustering of the disease profiles.
data(cytodisease)data(cytodisease)
A data frame with 85 observations on 4 variables.
Columns 1 and 2 contain the names of the nodes connected in the network. The third have the distances according to the GSEA scores and the fourth column is edge type the Running sum Peak Sign (RPS) for which 1 denotes positive correlation and (-1) a negative correlation.
http://www.ncbi.nlm.nih.gov/geo/
Barrett T et al. (2011) NCBI GEO: archive for func- tional genomics data sets-10 years on. Nucl. Acids Res, 39, D1005-D1010.
Iorio et al. (2010) Discovery of drug mode of action and drug repositioning from transcriptional responses. PNAS, 107(33), 14621- 14626.
data(cytodisease)data(cytodisease)
Data frame containing information for input into Cytoscape SIF file format. Contains the connections between the affinity propagation clustering of the drug profiles.
data(cytodrug)data(cytodrug)
A data frame with 1309 observations on 4 variables.
Columns 1 and 2 contain the names of the nodes connected in the network. The third have the distances according to the GSEA scores and the fourth column is edge type the Running sum Peak Sign (RPS) for which 1 denotes positive correlation and (-1) a negative correlation.
http://www.broadinstitute.org/genome_bio/connectivitymap.html
Lamb J et al. (2006) The Connectivity Map: Using Gene- Expression Signatures to Connect Small Molecules, Genes, and Disease. Science, 313(5795), 1929-1935.
Iorio et al. (2010) Discovery of drug mode of action and drug repositioning from transcriptional responses. PNAS, 107(33), 14621- 14626.
data(cytodrug)data(cytodrug)
Containing the names of the disease profiles and the numbers of the clusters for each node, as determined by affinity propagation clustering using GSEA scores for similarity matrix.
data(diseaseClusters)data(diseaseClusters)
A data frame with 85 observations on 2 variables.
Contains the cluster assignments for each of the disease profiles. The clusters were obtained using similarity scores from GSEA as input to the affinity propagation clustering method.
http://www.ncbi.nlm.nih.gov/geo/
http://www.ncbi.nlm.nih.gov/geo/
data(diseaseClusters)data(diseaseClusters)
Data frame containing the names of the experiments in the disease clusters, with the corresponding search terms to use in the MeSH browser through NCBI.
data(diseaselabels)data(diseaselabels)
Character matrix containing the names of the disease profiles in the DvDdata reference set in the first column [1]. Second column contains the corresponding search term that can be used in the MeSH browser.
http://www.ncbi.nlm.nih.gov/mesh/
[1] Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A. NCBI GEO: archive for functional genomics data sets 10 years on. Nucleic Acids Res. 2011 Jan;39(Database issue):D1005-10
data(diseaselabels)data(diseaselabels)
Ranked Lists by expression of genes for reference set of disease profiles.
data(diseaseRL)data(diseaseRL)
Matrix containing ranks of genes (rows) for a set of disease profiles (columns). The ranks are in decreasing order of differential expression.
http://www.ncbi.nlm.nih.gov/geo/
http://www.ncbi.nlm.nih.gov/geo/
data(diseaseRL)data(diseaseRL)
Containing the names of the drug profiles and the numbers of the clusters for each node, as determined by affinity propagation clustering using GSEA scores for similarity matrix.
data(drugClusters)data(drugClusters)
A data frame with 1309 observations on 2 variables.
A Data frame containing the names of the compounds in the DvDdata reference set in the first column. The second column contains the cluster they were assigned to using GSEA to calculate similarity between profiles used as input into affinity propagation clustering.
http://www.broadinstitute.org/genome_bio/connectivitymap.html
Lamb J et al. (2006) The Connectivity Map: Using Gene- Expression Signatures to Connect Small Molecules, Genes, and Disease. Science, 313(5795), 1929-1935.
Iorio et al. (2010) Discovery of drug mode of action and drug repositioning from transcriptional responses. PNAS, 107(33), 14621- 14626.
data(drugClusters)data(drugClusters)
Data frame containing the names of the compounds in the DvDdata drug profiles, with corresponding names to search the DrugBank [1] database through its web browser.
data(druglabels)data(druglabels)
http://www.broadinstitute.org/cmap/
[1] DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Wishart DS. Nucleic Acids Res. 2011 Jan;39(Database issue):D1035-41.
[2] The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease. Lamb J et al. Science 29 September 2006: 313 (5795), 1929-1935. [DOI:10.1126/science.1132939]
data(druglabels)data(druglabels)
Ranked Lists by expression of genes for reference set of drug profiles.
data(drugRL)data(drugRL)
A matrix containing the ranked lists of expression profiles for the 1309 drug compounds in the Connectivity Map (version 2) screening. Rows are the genes and the columns contain ranked lists for different drugs. The profiles are in rank decreasing order.
http://www.broadinstitute.org/genome_bio/connectivitymap.html
Lamb J et al. (2006) The Connectivity Map: Using Gene- Expression Signatures to Connect Small Molecules, Genes, and Disease. Science, 313(5795), 1929-1935.
Iorio et al. (2010) Discovery of drug mode of action and drug repositioning from transcriptional responses. PNAS, 107(33), 14621- 14626.
data(drugRL)data(drugRL)
List of HUGO genes included in the reference data sets.
data(genelist)data(genelist)
A character vector listing those genes in the reference data sets. Obtained using BioMart annotations of the Affymetrix HGU-133A, HGU-133A2 and HGU-133Plus2 platforms.
Durinck et al. (2009). Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nature Protocols 4, 1184-1191.
data(genelist)data(genelist)
List of possible factor values the GEO data sets can have.
data(GEOfactorvalues)data(GEOfactorvalues)
This character vector lists all the available experimental factors which are available in the GEO which can be used explanatory factors in a linear regression model.
http://www.ncbi.nlm.nih.gov/geo/
data(GEOfactorvalues)data(GEOfactorvalues)