| Title: | CAGE data from FANTOM3 and FANTOM4 projects |
|---|---|
| Description: | CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center. |
| Authors: | Vanja Haberle, Department of Biology, University of Bergen, Norway <[email protected]> |
| Maintainer: | Vanja Haberle <[email protected]> |
| License: | GPL-3 |
| Version: | 1.48.0 |
| Built: | 2026-10-10 11:06:50 UTC |
| Source: | https://github.com/bioc/FANTOM3and4CAGE |
A data.frame with information on all human CAGE samples from FANTOM3 and FANTOM4 projects available in this package.
data(FANTOMhumanSamples)data(FANTOMhumanSamples)
FANTOMhumanSamples is a data.frame with 3 columns:
dataset: the name of the dataset that can be loaded using data() function
group: the name of the group of samples that originate from the same tissue (e.g. blood)
sample: the name of the specific sample
The annotation of CAGE samples was obtained from the FANTOM web resource (http://fantom.gsc.riken.jp/4/download/).
Kawaji et al. (2010) Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation, Nucleic Acids Research 39:D856-D860.
data(FANTOMhumanSamples) head(FANTOMhumanSamples)data(FANTOMhumanSamples) head(FANTOMhumanSamples)
A data.frame with information on all mouse CAGE samples from FANTOM3 and FANTOM4 projects available in this package.
data(FANTOMmouseSamples)data(FANTOMmouseSamples)
FANTOMmouseSamples is a data.frame with 3 columns:
dataset: the name of the dataset that can be loaded using data() function
group: the name of the group of samples that originate from the same tissue (e.g. brain)
sample: the name of the specific sample
The annotation of CAGE samples was obtained from the FANTOM web resource (http://fantom.gsc.riken.jp/4/download/).
Kawaji et al. (2010) Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation, Nucleic Acids Research 39:D856-D860.
data(FANTOMmouseSamples) head(FANTOMmouseSamples)data(FANTOMmouseSamples) head(FANTOMmouseSamples)
This dataset contains all transcription start sites (TSSs) detected by CAGE and their frequency of usage in the human THP-1 cells induction timecourse from FANTOM4 project.
data(FANTOMtimecourseCAGEhuman)data(FANTOMtimecourseCAGEhuman)
FANTOMtimecourseCAGEhuman is a list with only one element (timecourse) named THP-1_monocytic_induction. This element is a data.frame with genomic positions of TSSs detected by CAGE and frequency of their usage in various timepoints during stimulation of human THP-1 myelomonocytic leukemia cells by phorbol myristate acetate (PMA). First three columns contain the chromosome (chr), the 1-based coordinate (pos) and the strand (strand) of the TSS, and the following columns contain the number of CAGE tags supporting that TSS in each specified timepoint.
The CAGE detected TSSs (mapped to the hg18 human genome assembly) and numbers of CAGE tags for THP-1 monocytic induction were obtained from the FANTOM web resource (http://fantom.gsc.riken.jp/4/download/). The data were originally published by The FANTOM Consortium (Suzuki et al., Nature Genetics 2009).
Kawaji et al. (2010) Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation, Nucleic Acids Research 39:D856-D860.
Suzuki et al. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line, Nature Genetics 41:553-562.
data(FANTOMtimecourseCAGEhuman) names(FANTOMtimecourseCAGEhuman) head(FANTOMtimecourseCAGEhuman[["THP-1_monocytic_induction"]])data(FANTOMtimecourseCAGEhuman) names(FANTOMtimecourseCAGEhuman) head(FANTOMtimecourseCAGEhuman[["THP-1_monocytic_induction"]])
This dataset contains all transcription start sites (TSSs) detected by CAGE and their frequency of usage in two mouse timecourses: adipogenic induction of DFAT-D1 preadipocytes and liver under constant darkness condition.
data(FANTOMtimecourseCAGEmouse)data(FANTOMtimecourseCAGEmouse)
FANTOMtimecourseCAGEmouse is a list with two elements (timecourses) named adipogenic_induction and liver_under_constant_darkness. Each element is a data.frame with genomic positions of TSSs detected by CAGE and frequency of their usage in various timepoints during timecourse. First three columns contain the chromosome (chr), the 1-based coordinate (pos) and the strand (strand) of the TSS, and the following columns contain the number of CAGE tags supporting that TSS in each specified timepoint.
The CAGE detected TSSs (mapped to the mm9 mouse genome assembly) and numbers of CAGE tags for both timecourses were obtained from the FANTOM web resource (http://fantom.gsc.riken.jp/4/download/). The data were originally published by The FANTOM Consortium (Carninci et al., Science 2005).
Kawaji et al. (2010) Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation, Nucleic Acids Research 39:D856-D860.
Carninci et al. (2005) The Transcriptional Landscape of the Mammalian Genome, Science 309(5740):1559-1563.
data(FANTOMtimecourseCAGEmouse) names(FANTOMtimecourseCAGEmouse) head(FANTOMtimecourseCAGEmouse[["adipogenic_induction"]])data(FANTOMtimecourseCAGEmouse) names(FANTOMtimecourseCAGEmouse) head(FANTOMtimecourseCAGEmouse[["adipogenic_induction"]])
This dataset contains all transcription start sites (TSSs) detected by CAGE and their frequency of usage in the various human tissues and cell lines generated in FANTOM3 and FANTOM4 projects.
data(FANTOMtissueCAGEhuman)data(FANTOMtissueCAGEhuman)
FANTOMtissueCAGEhuman is a list of groups of human samples, which are grouped by the tissue of origin. Each element is named according to the corresponding tissue and it is a data.frame with genomic positions of TSSs detected by CAGE and frequency of their usage in various samples originating from that tissue. First three columns in every data.frame contain the chromosome (chr), the 1-based coordinate (pos) and the strand (strand) of the TSS, and the following columns contain the number of CAGE tags supporting that TSS in each specific sample. These columns are named according to the corresponding sample.
The CAGE detected TSSs (mapped to the hg18 human genome assembly) and numbers of CAGE tags were obtained from the FANTOM web resource (http://fantom.gsc.riken.jp/4/download/). The data were originally published by The FANTOM Consortium (Carninci et al. Science 2005, and Carninci et al., Nature Genetics 2006, and Faulkner et al., Nature Genetics 2009).
Kawaji et al. (2010) Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation, Nucleic Acids Research 39:D856-D860.
Carninci et al. (2005) The transcriptional landscape of the mammalian genome, Science 309:1559-1563.
Carninci et al. (2006) Genome-wide analysis of mammalian promoter architecture and evolution, Nature Genetics 6:626-635.
Faulkner et al. (2009) The regulated retrotransposon transcriptome of mammalian cells, Nature Genetics 41:563-571.
data(FANTOMtissueCAGEhuman) names(FANTOMtissueCAGEhuman) head(FANTOMtissueCAGEhuman[["liver"]])data(FANTOMtissueCAGEhuman) names(FANTOMtissueCAGEhuman) head(FANTOMtissueCAGEhuman[["liver"]])
This dataset contains all transcription start sites (TSSs) detected by CAGE and their frequency of usage in the various mouse tissues and cell lines generated in FANTOM3 and FANTOM4 projects.
data(FANTOMtissueCAGEmouse)data(FANTOMtissueCAGEmouse)
FANTOMtissueCAGEmouse is a list of groups of mouse samples, which are grouped by the tissue of origin. Each element is named according to the corresponding tissue and it is a data.frame with genomic positions of TSSs detected by CAGE and frequency of their usage in various samples originating from that tissue. First three columns in every data.frame contain the chromosome (chr), the 1-based coordinate (pos) and the strand (strand) of the TSS, and the following columns contain the number of CAGE tags supporting that TSS in each specific sample. These columns are named according to the corresponding sample.
The CAGE detected TSSs (mapped to the mm9 mouse genome assembly) and numbers of CAGE tags were obtained from the FANTOM web resource (http://fantom.gsc.riken.jp/4/download/). The data were originally published by The FANTOM Consortium (Carninci et al., Science 2005, and Faulkner et al., Nature Genetics 2009).
Kawaji et al. (2010) Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation, Nucleic Acids Research 39:D856-D860.
Carninci et al. (2005) The transcriptional landscape of the mammalian genome, Science 309:1559-1563.
Faulkner et al. (2009) The regulated retrotransposon transcriptome of mammalian cells, Nature Genetics 41:563-571.
data(FANTOMtissueCAGEmouse) names(FANTOMtissueCAGEmouse) head(FANTOMtissueCAGEmouse[["lung"]])data(FANTOMtissueCAGEmouse) names(FANTOMtissueCAGEmouse) head(FANTOMtissueCAGEmouse[["lung"]])