| Type: | Package |
| Title: | The GANPA Datasets Package |
| Version: | 1.0 |
| Date: | 2011-05-26 |
| Author: | Zhaoyuan Fang, Weidong Tian and Hongbin Ji |
| Maintainer: | Zhaoyuan Fang <fangzhaoyuan@sibs.ac.cn> |
| Suggests: | GANPA |
| Description: | This is a dataset package for GANPA, which implements a network-based gene weighting approach to pathway analysis. This package includes data useful for GANPA, such as a functional association network, pathways, an expression dataset and multi-subunit proteins. |
| License: | GPL-2 |
| LazyLoad: | yes |
| Packaged: | 2012-10-29 08:57:06 UTC; ripley |
| Depends: | R (≥ 2.10) |
| Repository: | CRAN |
| Date/Publication: | 2012-10-29 08:57:06 |
| NeedsCompilation: | no |
The GANPA Datasets Package
Description
This is a dataset package for GANPA, which implements a network-based gene weighting approach to pathway analysis. This package includes data useful for GANPA, such as a functional association network, pathways, an expression dataset and multi-subunit proteins.
Details
| Package: | GANPAdata |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2011-05-26 |
| License: | GPL-2 |
| LazyLoad: | yes |
Author(s)
Zhaoyuan Fang, Weidong Tian and Hongbin Ji
Maintainer: Zhaoyuan Fang fangzhaoyuan@sibs.ac.cn
References
Zhaoyuan Fang, Weidong Tian and Hongbin Ji. A Network-Based Gene Weighting Approach for Pathway Analysis. Submitted.
Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, Scott L. Pomeroy, Todd R. Golub, Eric S. Lander, and Jill P. Mesirov. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS 2005 102(43): 15545-15550.
Gene expression data for the P53 dataset
Description
The P53 dataset is consisted of gene expression profiling of 17 P53-wildtype (WT) and 33 P53-mutated (MUT) cancer cell lines.
Usage
data(gExprs.p53)Format
A List of 2 matrices.
$ gExprs : num [1:10100, 1:50]
$ sampleinfo: chr [1:50, 1:2]
Source
http://www.broadinstitute.org/gsea/index.jsp
References
Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, Scott L. Pomeroy, Todd R. Golub, Eric S. Lander, and Jill P. Mesirov. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS 2005 102(43): 15545-15550.
Zhaoyuan Fang, Weidong Tian and Hongbin Ji. A Network-Based Gene Weighting Approach for Pathway Analysis. Submitted.
Examples
data(gExprs.p53)
gNET: A comprehensive gene functional association network
Description
gNET was constructed from protein-protein interactions (PPI), co-annotation in GO Biological Process (BP), and co-expression in large scale gene expression microarray data. Several limits have been applied to these data sources to achieve specificity.
Usage
data(gNET)Format
A List of 16979 character vectors.
References
Zhaoyuan Fang, Weidong Tian and Hongbin Ji. A Network-Based Gene Weighting Approach for Pathway Analysis. Submitted.
Examples
data(gNET)
Functional Gene Sets Used in GSEA PNAS Publication
Description
A list of 522 C2 functional gene sets, see reference for details.
Usage
data(gsets.msigdb.pnas)Format
A List of 522 character vectors.
Source
http://www.broadinstitute.org/gsea/index.jsp
References
Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, Scott L. Pomeroy, Todd R. Golub, Eric S. Lander, and Jill P. Mesirov. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS 2005 102(43): 15545-15550.
Examples
data(gsets.msigdb.pnas)
A List of Human Multi-subunit Proteins
Description
A list of genes encoding 82 multi-subunit proteins were extracted from human genes.
Usage
data(msp.groups)Format
A List of 82 character vectors.
Details
A multi-subunit protein is named in the format of Multi.XXX where XXX is a member gene picked arbitrarily from the subunit gene group. Note this naming rule is just for convenience.
References
Zhaoyuan Fang, Weidong Tian and Hongbin Ji. A Network-Based Gene Weighting Approach for Pathway Analysis. Submitted.
Examples
data(msp.groups)