| Title: | 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. |
| Authors: | Zhaoyuan Fang, Weidong Tian and Hongbin Ji |
| Maintainer: | Zhaoyuan Fang <[email protected]> |
| License: | GPL-2 |
| Version: | 1.0 |
| Built: | 2025-02-13 03:41:09 UTC |
| Source: | https://github.com/cran/GANPAdata |
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.
| Package: | GANPAdata |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2011-05-26 |
| License: | GPL-2 |
| LazyLoad: | yes |
Zhaoyuan Fang, Weidong Tian and Hongbin Ji
Maintainer: Zhaoyuan Fang [email protected]
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.
The P53 dataset is consisted of gene expression profiling of 17 P53-wildtype (WT) and 33 P53-mutated (MUT) cancer cell lines.
data(gExprs.p53)data(gExprs.p53)
A List of 2 matrices.
$ gExprs : num [1:10100, 1:50]
$ sampleinfo: chr [1:50, 1:2]
http://www.broadinstitute.org/gsea/index.jsp
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.
data(gExprs.p53)data(gExprs.p53)
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.
data(gNET)data(gNET)
A List of 16979 character vectors.
Zhaoyuan Fang, Weidong Tian and Hongbin Ji. A Network-Based Gene Weighting Approach for Pathway Analysis. Submitted.
data(gNET)data(gNET)
A list of 522 C2 functional gene sets, see reference for details.
data(gsets.msigdb.pnas)data(gsets.msigdb.pnas)
A List of 522 character vectors.
http://www.broadinstitute.org/gsea/index.jsp
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.
data(gsets.msigdb.pnas)data(gsets.msigdb.pnas)
A list of genes encoding 82 multi-subunit proteins were extracted from human genes.
data(msp.groups)data(msp.groups)
A List of 82 character vectors.
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.
Zhaoyuan Fang, Weidong Tian and Hongbin Ji. A Network-Based Gene Weighting Approach for Pathway Analysis. Submitted.
data(msp.groups)data(msp.groups)