CAGEr 2.2.0
Note: this still uses the CAGEset class.
There are several large collections of CAGE data available that provide single base-pair resolution TSSs for numerous human and mouse primary cells, cell lines and tissues. Together with several minor datasets for other model organisms (Drosophila melanogaster, Danio rerio) they are a valuable resource that provides cell/tissue type and developmental stage specific TSSs essential for any type of promoter centred analysis. By enabling direct and user-friendly import of TSSs for selected samples into R, CAGEr facilitates the integration of these precise TSS data with other genomic data types. Each of the available CAGE data resources accessible from within CAGEr is explained in more detail further below.
FANTOM consortium provides single base-pair resolution TSS data for numerous
human and mouse primary cells, cell lines and tissues. The main FANTOM5
publication (Consortium 2014) released ~1000 human and ~400 mouse CAGE
samples that cover the vast majority of human primary cell types, mouse
developmental tissues and a large number of commonly used cell lines. These data
is available from FANTOM web resource http://fantom.gsc.riken.jp/5/data/ in
the form of TSS files with genomic coordinates and number of tags mapping to
each TSS detected by CAGE. The list of all available samples for both human and
mouse (as presented in the Supplementary Table 1 of the publication) has been
included in CAGEr to facilitate browsing, searching and selecting samples
of interest. TSSs for selected samples are then fetched directly form the web
resource and imported into a CAGEset object enabling their further
manipulation with CAGEr.
Previous FANTOM projects (3 and 4) (Consortium 2005, @Faulkner:2009fw, @Suzuki:2009gy))
produced CAGE datasets for multiple human and mouse tissues as well as several
timecourses, including differentiation of a THP-1 human myeloid leukemia cell
line. All this TSS data has been grouped into datasets by the organism and
tissue of origin and has been collected into an R data package named
FANTOM3and4CAGE, which is available from Bioconductor https://bioconductor.org/packages/FANTOM3and4CAGE.
The vignette accompanying the package provides information on available datasets
and lists of samples. When the data package is installed, CAGEr can import the
TSSs for selected samples directly into a CAGEset object for further
manipulation.
ENCODE consortium produced CAGE data for common human cell lines (Djebali et al. 2012), which were used by ENCODE for various other types of genome-wide analyses. The advantage of this dataset is that it enables the integration of precise TSSs from a specific cell line with many other genome-wide data types provided by ENCODE for the same cell line. However, the format of CAGE data provided by ENCODE at UCSC (http://genome.ucsc.edu/ENCODE/dataMatrix/encodeDataMatrixHuman.html) includes only raw mapped CAGE tags and their coverage along the genome, and coordinates of enriched genomic regions (peaks), which do not take advantage of the single base-pair resolution provided by CAGE. To address this, we have used the raw CAGE tags to derive single base-pair resolution TSSs and collected them into an R data package named ENCODEprojectCAGE. This data package is available for download from CAGEr web site at http://promshift.genereg.net/CAGEr and includes TSSs for 36 different cell lines fractionated by cellular compartment. The vignette accompanying the package provides information on available datasets and lists of individual samples. Once the package has been downloaded and installed, CAGEr can access it to import TSS data for selected subset of samples for further manipulation and integration.
Precise TSSs are also available for zebrafish (Danio Rerio) from CAGE data
published by (Nepal et al. 2013). The timecourse covering early
embryonic development of zebrafish includes 12 developmental stages. The TSS
data has been collected into an R data package named ZebrafishDevelopmentalCAGE,
which is available for download from CAGEr web site at http://promshift.genereg.net/CAGEr.
As with other data packages mentioned above, once the package is installed
CAGEr can use it to import stage-specific single base pair TSSs into a
CAGEset object.
Note: this still uses the CAGEset class.
The data from above mentioned resources can be imported into a CAGEset object
using the importPublicData() function. It function has four arguments: source,
dataset, group and sample. Argument source accepts one of the following
values: "FANTOM5", "FANTOM3and4", "ENCODE", or "ZebrafishDevelopment",
which refer to one of the four resources listed above. The following sections
explain how to utilize this function for each of the four currently supported
resources.
Lists of all human and mouse CAGE samples produced within FANTOM5 project are available in CAGEr. To load the information on human samples type:
library(CAGEr)
data(FANTOM5humanSamples)
head(FANTOM5humanSamples)## sample type
## 143 acantholytic_squamous_carcinoma_cell_line_HCC1806 cell line
## 46 acute_lymphoblastic_leukemia__B-ALL__cell_line_BALL-1 cell line
## 75 acute_lymphoblastic_leukemia__B-ALL__cell_line_NALM-6 cell line
## 24 acute_lymphoblastic_leukemia__T-ALL__cell_line_HPB-ALL cell line
## 48 acute_lymphoblastic_leukemia__T-ALL__cell_line_Jurkat cell line
## 250 acute_myeloid_leukemia__FAB_M0__cell_line_Kasumi-3 cell line
## description library_id
## 143 acantholytic squamous carcinoma cell line:HCC1806 CNhs11844
## 46 acute lymphoblastic leukemia (B-ALL) cell line:BALL-1 CNhs11251
## 75 acute lymphoblastic leukemia (B-ALL) cell line:NALM-6 CNhs11282
## 24 acute lymphoblastic leukemia (T-ALL) cell line:HPB-ALL CNhs10746
## 48 acute lymphoblastic leukemia (T-ALL) cell line:Jurkat CNhs11253
## 250 acute myeloid leukemia (FAB M0) cell line:Kasumi-3 CNhs13241
## data_url
## 143 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/acantholytic%2520squamous%2520carcinoma%2520cell%2520line%253aHCC1806.CNhs11844.10717-109I6.hg19.ctss.bed.gz
## 46 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/acute%2520lymphoblastic%2520leukemia%2520%2528B-ALL%2529%2520cell%2520line%253aBALL-1.CNhs11251.10455-106G5.hg19.ctss.bed.gz
## 75 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/acute%2520lymphoblastic%2520leukemia%2520%2528B-ALL%2529%2520cell%2520line%253aNALM-6.CNhs11282.10534-107G3.hg19.ctss.bed.gz
## 24 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/acute%2520lymphoblastic%2520leukemia%2520%2528T-ALL%2529%2520cell%2520line%253aHPB-ALL.CNhs10746.10429-106D6.hg19.ctss.bed.gz
## 48 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/acute%2520lymphoblastic%2520leukemia%2520%2528T-ALL%2529%2520cell%2520line%253aJurkat.CNhs11253.10464-106H5.hg19.ctss.bed.gz
## 250 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.LQhCAGE/acute%2520myeloid%2520leukemia%2520%2528FAB%2520M0%2529%2520cell%2520line%253aKasumi-3.CNhs13241.10789-110H6.hg19.ctss.bed.gznrow(FANTOM5humanSamples)## [1] 988There are 988 human samples in total and for each the following information is provided:
sample: a unique name/label of the sample which should be provided to
importPublicData() function to retrieve given sample
type: type of sample, which can be “cell line”, “primary cell” or “tissue”
description: short description of the sample as provided in FANTOM5 main
publication (Consortium 2014)
library_id: unique ID of the CAGE library within FANTOM5
data_url: URL to corresponding CTSS file at FANTOM5 web resource from which
the data is fetched
Provided information facilitates searching for samples of interest, e.g. we can search for astrocyte samples:
astrocyteSamples <- FANTOM5humanSamples[grep("Astrocyte",
FANTOM5humanSamples[,"description"]),]
astrocyteSamples## sample type
## 343 Astrocyte_-_cerebellum__donor1 primary cell
## 537 Astrocyte_-_cerebellum__donor2 primary cell
## 562 Astrocyte_-_cerebellum__donor3 primary cell
## 286 Astrocyte_-_cerebral_cortex__donor1 primary cell
## 429 Astrocyte_-_cerebral_cortex__donor2 primary cell
## 472 Astrocyte_-_cerebral_cortex__donor3 primary cell
## description library_id
## 343 Astrocyte - cerebellum, donor1 CNhs11321
## 537 Astrocyte - cerebellum, donor2 CNhs12081
## 562 Astrocyte - cerebellum, donor3 CNhs12117
## 286 Astrocyte - cerebral cortex, donor1 CNhs10864
## 429 Astrocyte - cerebral cortex, donor2 CNhs11960
## 472 Astrocyte - cerebral cortex, donor3 CNhs12005
## data_url
## 343 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Astrocyte%2520-%2520cerebellum%252c%2520donor1.CNhs11321.11500-119F6.hg19.ctss.bed.gz
## 537 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Astrocyte%2520-%2520cerebellum%252c%2520donor2.CNhs12081.11580-120F5.hg19.ctss.bed.gz
## 562 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Astrocyte%2520-%2520cerebellum%252c%2520donor3.CNhs12117.11661-122F5.hg19.ctss.bed.gz
## 286 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Astrocyte%2520-%2520cerebral%2520cortex%252c%2520donor1.CNhs10864.11235-116D2.hg19.ctss.bed.gz
## 429 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Astrocyte%2520-%2520cerebral%2520cortex%252c%2520donor2.CNhs11960.11316-117D2.hg19.ctss.bed.gz
## 472 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Astrocyte%2520-%2520cerebral%2520cortex%252c%2520donor3.CNhs12005.11392-118C6.hg19.ctss.bed.gzdata(FANTOM5mouseSamples)
head(FANTOM5mouseSamples)## sample
## 144 J2E_erythroblastic_leukemia_response_to_erythropoietin__00hr00min__biol_rep1
## 145 J2E_erythroblastic_leukemia_response_to_erythropoietin__00hr00min__biol_rep2
## 146 J2E_erythroblastic_leukemia_response_to_erythropoietin__00hr00min__biol_rep3
## 91 Atoh1+_Inner_ear_hair_cells_-_organ_of_corti__pool1
## 111 CD326+_enterocyte_isolated_from_mice__treated_with_RANKL__day03__pool1
## 109 CD326++_enterocyte_isolated_from_mice__treated_with_RANKL__day03__pool1
## type
## 144 cell line
## 145 cell line
## 146 cell line
## 91 primary cell
## 111 primary cell
## 109 primary cell
## description
## 144 J2E erythroblastic leukemia response to erythropoietin, 00hr00min, biol_rep1
## 145 J2E erythroblastic leukemia response to erythropoietin, 00hr00min, biol_rep2
## 146 J2E erythroblastic leukemia response to erythropoietin, 00hr00min, biol_rep3
## 91 Atoh1+ Inner ear hair cells - organ of corti, pool1
## 111 CD326+ enterocyte isolated from mice, treated with RANKL, day03, pool1
## 109 CD326++ enterocyte isolated from mice, treated with RANKL, day03, pool1
## library_id
## 144 CNhs12449
## 145 CNhs12668
## 146 CNhs12770
## 91 CNhs12533
## 111 CNhs13242
## 109 CNhs13236
## data_url
## 144 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/J2E%2520erythroblastic%2520leukemia%2520response%2520to%2520erythropoietin%252c%252000hr00min%252c%2520biol_rep1.CNhs12449.13063-139I3.mm9.ctss.bed.gz
## 145 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/J2E%2520erythroblastic%2520leukemia%2520response%2520to%2520erythropoietin%252c%252000hr00min%252c%2520biol_rep2.CNhs12668.13129-140G6.mm9.ctss.bed.gz
## 146 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/J2E%2520erythroblastic%2520leukemia%2520response%2520to%2520erythropoietin%252c%252000hr00min%252c%2520biol_rep3.CNhs12770.13195-141E9.mm9.ctss.bed.gz
## 91 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Atoh1%252b%2520Inner%2520ear%2520hair%2520cells%2520-%2520organ%2520of%2520corti%252c%2520pool1.CNhs12533.12158-128G7.mm9.ctss.bed.gz
## 111 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/CD326%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool1.CNhs13242.11850-124I5.mm9.ctss.bed.gz
## 109 http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool1.CNhs13236.11852-124I7.mm9.ctss.bed.gznrow(FANTOM5mouseSamples)## [1] 395To import TSS data for samples of interest from FANTOM5 we use the importPublicData()
function and set the argument source = "FANTOM5". The dataset argument can
be set to either "human" or "mouse", and the sample argument is provided
by a vector of sample lables/names. For example, names of astrocyte samples from
above are:
astrocyteSamples[,"sample"]## [1] "Astrocyte_-_cerebellum__donor1" "Astrocyte_-_cerebellum__donor2"
## [3] "Astrocyte_-_cerebellum__donor3" "Astrocyte_-_cerebral_cortex__donor1"
## [5] "Astrocyte_-_cerebral_cortex__donor2" "Astrocyte_-_cerebral_cortex__donor3"and to import first three samples type:
astrocyteCAGEset <- importPublicData(source = "FANTOM5", dataset = "human",
sample = astrocyteSamples[1:3,"sample"])The resulting astrocyteCAGEset is a CAGEset object that can be included in
the CAGEr workflow described above to perform normalisation, clustering,
visualisation, etc.
To use TSS data from FANTOM3 and FANTOM4 projects, a data package FANTOM3and4CAGE has to be installed and loaded. This package is available from Bioconductor and can be installed by calling:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("FANTOM3and4CAGE")For the list of available datasets with group and sample labels for specific human or mouse samples load the data package and get list of samples:
library(FANTOM3and4CAGE)
data(FANTOMhumanSamples)
head(FANTOMhumanSamples)## dataset group sample
## 1 FANTOMtissueCAGEhuman cerebrum cerebrum
## 2 FANTOMtissueCAGEhuman renal_artery renal_artery
## 3 FANTOMtissueCAGEhuman ureter ureter
## 4 FANTOMtissueCAGEhuman urinary_bladder urinary_bladder
## 5 FANTOMtissueCAGEhuman kidney malignancy
## 6 FANTOMtissueCAGEhuman kidney kidneydata(FANTOMmouseSamples)
head(FANTOMmouseSamples)## dataset group
## 1 FANTOMtissueCAGEmouse brain
## 2 FANTOMtissueCAGEmouse brain
## 3 FANTOMtissueCAGEmouse brain
## 4 FANTOMtissueCAGEmouse brain
## 5 FANTOMtissueCAGEmouse cerebral_cortex
## 6 FANTOMtissueCAGEmouse hippocampus
## sample
## 1 brain
## 2 CCL-131_Neuro-2a_control
## 3 CCL-131_Neuro-2a_treatment_for_6hr_with_MPP+
## 4 CCL-131_Neuro-2a_treatment_for_12hr_with_MPP+
## 5 cerebral_cortex
## 6 hippocampusIn the above data frames, the columns dataset, group and sample provide
values that should be passed to corresponding arguments in importPublicData()
function. For example to import human kidney normal and malignancy samples call:
kidneyCAGEset <- importPublicData(source = "FANTOM3and4",
dataset = "FANTOMtissueCAGEhuman",
group = "kidney", sample = c("kidney", "malignancy"))When the samples belong to different groups or different datasets, it is necessary to provide the dataset and group assignment for each sample separately:
mixedCAGEset <- importPublicData(source = "FANTOM3and4",
dataset = c("FANTOMtissueCAGEmouse", "FANTOMtissueCAGEmouse",
"FANTOMtimecourseCAGEmouse"), group = c("liver", "liver",
"liver_under_constant_darkness"),
sample = c("cloned_mouse", "control_mouse", "4_hr"))For more details about datasets available in the data package please refer to the vignette accompanying the package.
TSS data derived from ENCODE CAGE datasets has been collected into
ENCODEprojectCAGE data package, which is available for download from the
CAGEr web site (http://promshift.genereg.net/CAGEr/). Downloaded package can
be installed from local using install.packages() function from within R and
used with CAGEr as described below.
List of datasets available in this data package can be obtained like this:
library(ENCODEprojectCAGE)
data(ENCODEhumanCellLinesSamples)The information provided in this data frame is analogous to the one in previously discussed data package and provides values to be used with importPublicData() function. The command to import whole cell CAGE samples for three different cell lines would look like this:
ENCODEset <- importPublicData(source = "ENCODE",
dataset = c("A549", "H1-hESC", "IMR90"),
group = c("cell", "cell", "cell"), sample = c("A549_cell_rep1",
"H1-hESC_cell_rep1", "IMR90_cell_rep1"))For more details about datasets available in the ENCODEprojectCAGE data package please refer to the vignette accompanying the package.
The zebrafish TSS data for 12 developmental stages is collected in
ZebrafishDevelopmentalCAGE data package, which is also available for download
from the CAGEr web site (http://promshift.genereg.net/CAGEr/). It can be
installed from local using install.packages() function. To get a list of
samples within the package type:
library(ZebrafishDevelopmentalCAGE)
data(ZebrafishSamples)In this package there is only one dataset called ZebrafishCAGE and all samples
belong to the same group called development. To import selected samples from
this dataset type:
zebrafishCAGEset <- importPublicData(source = "ZebrafishDevelopment",
dataset = "ZebrafishCAGE", group = "development",
sample = c("zf_64cells", "zf_prim6"))For more details please refer to the vignette accompanying the data package.
Importing TSS data from any of the four above explained resources results in the
CAGEset object that can be directly included into the workflow provided by
CAGEr to perform normalisation, clustering, promoter width analysis,
visualisation, etc. This high-resolution TSS data can then easily be
integrated with other genomic data types to perform various promoter-centred
analyses, which does not rely on annotation but uses precise and matched
cell/tissue type TSSs.
sessionInfo()## R version 4.2.0 RC (2022-04-19 r82224)
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## Running under: macOS Mojave 10.14.6
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## [8] base
##
## other attached packages:
## [1] FANTOM3and4CAGE_1.31.0 CAGEr_2.2.0
## [3] MultiAssayExperiment_1.22.0 SummarizedExperiment_1.26.0
## [5] Biobase_2.56.0 GenomicRanges_1.48.0
## [7] GenomeInfoDb_1.32.0 IRanges_2.30.0
## [9] S4Vectors_0.34.0 BiocGenerics_0.42.0
## [11] MatrixGenerics_1.8.0 matrixStats_0.62.0
## [13] BiocStyle_2.24.0
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## loaded via a namespace (and not attached):
## [1] nlme_3.1-157 bitops_1.0-7
## [3] tools_4.2.0 bslib_0.3.1
## [5] vegan_2.6-2 utf8_1.2.2
## [7] R6_2.5.1 KernSmooth_2.23-20
## [9] mgcv_1.8-40 DBI_1.1.2
## [11] colorspace_2.0-3 permute_0.9-7
## [13] tidyselect_1.1.2 compiler_4.2.0
## [15] cli_3.3.0 DelayedArray_0.22.0
## [17] rtracklayer_1.56.0 bookdown_0.26
## [19] sass_0.4.1 scales_1.2.0
## [21] stringr_1.4.0 digest_0.6.29
## [23] Rsamtools_2.12.0 rmarkdown_2.14
## [25] stringdist_0.9.8 XVector_0.36.0
## [27] pkgconfig_2.0.3 htmltools_0.5.2
## [29] sparseMatrixStats_1.8.0 fastmap_1.1.0
## [31] BSgenome_1.64.0 rlang_1.0.2
## [33] VGAM_1.1-6 DelayedMatrixStats_1.18.0
## [35] jquerylib_0.1.4 BiocIO_1.6.0
## [37] generics_0.1.2 jsonlite_1.8.0
## [39] BiocParallel_1.30.0 gtools_3.9.2
## [41] dplyr_1.0.8 RCurl_1.98-1.6
## [43] magrittr_2.0.3 GenomeInfoDbData_1.2.8
## [45] Matrix_1.4-1 Rcpp_1.0.8.3
## [47] munsell_0.5.0 fansi_1.0.3
## [49] lifecycle_1.0.1 stringi_1.7.6
## [51] yaml_2.3.5 MASS_7.3-57
## [53] zlibbioc_1.42.0 plyr_1.8.7
## [55] grid_4.2.0 formula.tools_1.7.1
## [57] parallel_4.2.0 crayon_1.5.1
## [59] lattice_0.20-45 Biostrings_2.64.0
## [61] splines_4.2.0 knitr_1.38
## [63] pillar_1.7.0 rjson_0.2.21
## [65] codetools_0.2-18 reshape2_1.4.4
## [67] XML_3.99-0.9 glue_1.6.2
## [69] evaluate_0.15 data.table_1.14.2
## [71] BiocManager_1.30.17 operator.tools_1.6.3
## [73] vctrs_0.4.1 gtable_0.3.0
## [75] purrr_0.3.4 assertthat_0.2.1
## [77] cachem_1.0.6 ggplot2_3.3.5
## [79] xfun_0.30 restfulr_0.0.13
## [81] tibble_3.1.6 som_0.3-5.1
## [83] GenomicAlignments_1.32.0 memoise_2.0.1
## [85] cluster_2.1.3 ellipsis_0.3.2Consortium, The FANTOM. 2005. “The Transcriptional Landscape of the Mammalian Genome.” Science 309 (5740): 1559–63.
———. 2014. “A promoter-level mammalian expression atlas.” Nature 507 (7493): 462–70.
Djebali, Sarah, Carrie A Davis, Angelika Merkel, Alex Dobin, Timo Lassmann, Ali Mortazavi, Andrea Tanzer, et al. 2012. “Landscape of transcription in human cells.” Nature 488 (7414): 101–8.
Faulkner, Geoffrey J, Yasumasa Kimura, Carsten O Daub, Shivangi Wani, Charles Plessy, Katharine M Irvine, Kate Schroder, et al. 2009. “The regulated retrotransposon transcriptome of mammalian cells.” Nature Genetics 41 (5): 563–71.
Nepal, Chirag, Yavor Hadzhiev, Christopher Previti, Vanja Haberle, Nan Li, Hazuki Takahashi, Ana Maria S. Suzuki, et al. 2013. “Dynamic regulation of coding and non-coding transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis.” Genome Research 23 (11): 1938–50.
Suzuki, Harukazu, Alistair R R Forrest, Erik van Nimwegen, Carsten O Daub, Piotr J Balwierz, Katharine M Irvine, Timo Lassmann, et al. 2009. “The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.” Nature Genetics 41 (5): 553–62.