,
Julie Devis [aut] ,
Anna Diacofotaki [ctb],
Charles De Smet [ths],
Laurent Gatto [aut, ths, cre] | Title: | Data companion to CTexploreR |
|---|---|
| Description: | Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics. |
| Authors: | Axelle Loriot [aut] ,
Julie Devis [aut] ,
Anna Diacofotaki [ctb],
Charles De Smet [ths],
Laurent Gatto [aut, ths, cre] |
| Maintainer: | Laurent Gatto <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.7.0 |
| Built: | 2024-10-30 05:22:43 UTC |
| Source: | https://github.com/bioc/CTdata |
All genes description, according to the analysis done for CT genes
A tibble object with 24488 rows and 47 columns.
Rows correspond to genes
Columns give genes characteristics
When the promoter is mentionned, it has been determined as 1000 nt upstream TSS and 200 nt downstream TSS.
CT_genes characteristics column:
Column CT_gene_type indicates if the gene is a CT specific gene
("CT_gene" : testis_specific in testis_specificity) and activated in
"TCGA_category" and "CCLE_category) or CT preferential gene ("CTP_gene" :
testis_preferential in testis_specificity) and activated in"TCGA_category"
and "CCLE_category").
Column testis_specificity gives the testis-specificity of genes
assigned to each gene using GTEX_category and multimapping_analysis
("testis_specific" or "testis_preferential"). Genes were assigned
"testis-preferential" if testis-specific in these categories but not testis
specific in HPA_category or leaky in CCLE_category or TCGA_category.
Column regulated_by_methylation indicates if the gene is
regulated by methylation (TRUE) based on DAC induction (has to
be TRUE) and on promoter methylation level in normal somatic tissues
(when available, has to be methylated in somatic tissues).
Column X_linked indicates if the gene is on the chromosome X
(TRUE) or not (FALSE).
Columns chr, strand and transcription_start_site give the
genomic location.
Column GTEX_category gives the category ("testis_specific",
"testis_preferential" or "lowly_expressed") assigned to each gene
using GTEx database (see ?GTEX_data for details).
Column q75_TPM_somatic gives the q75 expression level found
in a somatic tissue (using GTEx database).
Column max_TPM_somatic gives the maximum expression level found
in a somatic tissue (using GTEx database).
Column ratio_testis_somatic gives the ratio between expression in testis
and the highest expression found in a somatic tissue (using GTEx database).
Column TPM_testis gives the gene expression level in testis
(using GTEx database).
Column lowly_expressed_in_GTEX indicates if the gene is lowly
expressed in GTEX database and thus needed to be analysed with
multimapping allowed.
Column multimapping_analysis informs if the gene (flagged as
"lowly_expressed" in GTEX_data) was found to be testis-specific
when multi-mapped reads were counted for gene expression in
normal tissues ("not_analysed" or "testis_specific") (see
?normal_tissues_multimapping_data for details).
Column HPA_RNA_single_cell_type_specific_nTPM specifies the cell types in
which genes were detected in the HPA single cell data (see
?HPA_cell_type_specificity for details).
Column max_HPA_germcell specifies if the maximum expression value in a
germ cell type. (see ?HPA_cell_type_specificity for details).
Column max_HPA_somatic specifies if the maximum expression value in a
somatic cell type. (see ?HPA_cell_type_specificity for details).
Column not_detected_in_somatic_HPA specifies if the gene is detected or
not in a somatic cell type. (see ?HPA_cell_type_specificity for details).
Column HPA_ratio_germ_som gives the ratio between max_HPA_germcell and
max_HPA_somatic columns.
Column percent_of_positive_CCLE_cell_lines gives the percentage
of CCLE cancer cell lines in which genes are expressed (genes
were considered as expressed if TPM >= 1).
Column percent_of_negative_CCLE_cell_lines gives the percentage
of CCLE cancer cell lines in which genes are repressed (TPM <=
0.5).
Column max_TPM_in_CCLE gives the highest expression level of
genes in CCLE cell lines.
Column CCLE_category gives the category assigned to each gene
using CCLE data. "Activated" category corresponds to genes
expressed in at least 1% of cell lines (TPM >= 1) and repressed in
at least 20% of cell lines.
Column percent_pos_tum gives the percentage of TCGA cancer
samples in which genes are expressed (genes were considered as
expressed if TPM >= 1).
Column percent_neg_tum gives the percentage of TCGA cancer samples in
which genes are repressed (TPM <= 0.5).
Column max_TPM_in_TCGA gives the highest expression level of
genes in TCGA cancer sample.
Column max_q75_in_NT gives the maximum q75 expression in normal
peritumoral tissues from TCGA.
Column TCGA_category gives the category assigned to each gene
using TCGA data. "activated" category corresponds to genes
expressed in at least 1% of tumors (TPM >= 1) and repressed in at
least 20% of samples. "multimapping_issue" corresponds to genes
that need multi-mapping to be allowed in order to be analysed
properly.
Columns external_transcript_name, ensembl_transcript_id, and
transcript_biotype give the references and informations about
the most biologically relevant transcript associated to each
gene.
Column IGV_backbone indicates if a gene has been removed from CT genes
as RNA-Seq reads were not properly aligned on exons, but were instead
spread across a wide genomic region spanning the genes.
Column family gives the gene family name.
Column DAC_induced summarises the results (TRUE or FALSE)
of a differential expression evaluating gene induction upon DAC
treatment in a series of cell lines.
Column named CpG_density, gives the density of CpG within each
promoter (number of CpG / promoter length * 100).
Column CpG_promoter classifies the promoters according to their
CpG densities: "low" (CpG_density < 2), "intermediate"
(CpG_density >= 2 & CpG_density < 4), and "high" (CpG_density >=
4).
Column somatic_met_level that gives the mean methylation level
of each promoter in somatic tissues.
Column sperm_met_level that gives the methylation level of each
promoter in sperm.
Column somatic_methylation indicates if the promoter's mean
methylation level in somatic tissues is higher than 50%.
Column germline_methylationindicates if the promoter is
methylated in germline, based on the ratio with somatic tissues
(FALSE if somatic_met_level is at least twice higher than
germline_met_level).
Columns oncogene and tumor_suppressor informs if oncogenic
and tumor-suppressor functions have been associated to genes
(source: Cancermine).
See scripts/make_all_genes_prelim.R and
scripts/make_all_genes_and_CT_genes.R for details on how this list of genes
was created.
Correlation coefficients between Cancer-Testis genes and all genes found on the CCLE database.
A matrix object with 238 rows and 24483 columns.
Rows correspond to CT genes
Columns correspond to all genes from CCLE database
Correlation coefficients (Pearson) between CT genes and all other
genes are given in the matrix. These correlation coefficients were
calculated using log transformed expression values from CCLE_data
(all cell lines).
See scripts/make_CCLE_correlation_matrix.R for details.
Gene expression data in cancer cell lines from CCLE
A SummarizedExperiment object with 24473 rows and 1229 columns
Rows correspond to genes (ensembl_gene_id)
Columns correspond to CCLE cell lines
Expression data from the assay are TPM values
Cell lines metadata are stored in colData
The rowData contains
A column percent_of_positive_CCLE_cell_lines that gives the
percentage of CCLE cell lines (all cell lines combined)
expressing the gene (TPM >= 1).
A column percent_of_negative_CCLE_cell_lines that gives the
percent of CCLE cell lines (all cell lines combined) in which
genes are repressed (TPM < 0.5)
A column max_TPM_in_CCLE that gives the maximal expression (in
TPM) found in all cell lines.
A column CCLE_category gives the category ("activated",
"not_activated", "leaky") assigned to each gene. "activated"
category corresponds to genes expressed (TPM >= 1) in at
least 1% of cell lines, repressed (TPM <= 0.5) in at least 20% of
cell lines with a maximal expression higher than 5 TPM.
"not_activated" category corresponds to genes
repressed (TPM <= 0.5) in at least 20% of cell lines but
expressed (TPM >= 1) less than 1%. "leaky" category
corresponds to genes repressed (TPM <= 0.5) in less than 20% of
cell lines. "lowly_expressed" corresponds to genes repressed (TPM <= 0.5)
in at least 20%, expressed (TPM >= 1) in more than 1 % of cell lines, with
a maximum expression lower than 5 TPM.
TPM values downloaded using depmap bioconductor package (see
scripts/make_CCLE_data.R for details).
Cancer-Testis (CT) genes description
A tibble object with 280 rows and 47 columns.
Rows correspond to CT genes
Columns give CT genes characteristics
When the promoter is mentionned, it has been determined as 1000 nt upstream TSS and 200 nt downstream TSS.
CT_genes characteristics column:
Column CT_gene_type indicates if the gene is a CT specific gene
("CT_gene" : testis_specific in testis_specificity) and activated in
"TCGA_category" and "CCLE_category) or CT preferential gene ("CTP_gene" :
testis_preferential in testis_specificity) and activated in"TCGA_category"
and "CCLE_category").
Column testis_specificity gives the testis-specificity of genes
assigned to each gene using GTEX_category and multimapping_analysis
("testis_specific" or "testis_preferential"). Genes were assigned
"testis-preferential" if testis-specific in these categories but not testis
specific in HPA_category or leaky in CCLE_category or TCGA_category.
Column regulated_by_methylation indicates if the gene is
regulated by methylation (TRUE) based on DAC induction (has to
be TRUE) and on promoter methylation level in normal somatic tissues
(when available, has to be methylated in somatic tissues).
Column X_linked indicates if the gene is on the chromosome X
(TRUE) or not (FALSE).
Columns chr, strand and transcription_start_site give the
genomic location.
Column GTEX_category gives the category ("testis_specific",
"testis_preferential" or "lowly_expressed") assigned to each gene
using GTEx database (see ?GTEX_data for details).
Column q75_TPM_somatic gives the q75 expression level found
in a somatic tissue (using GTEx database).
Column max_TPM_somatic gives the maximum expression level found
in a somatic tissue (using GTEx database).
Column ratio_testis_somatic gives the ratio between expression in testis
and the highest expression found in a somatic tissue (using GTEx database).
Column TPM_testis gives the gene expression level in testis
(using GTEx database).
Column lowly_expressed_in_GTEX indicates if the gene is lowly
expressed in GTEX database and thus needed to be analysed with
multimapping allowed.
Column multimapping_analysis informs if the gene (flagged as
"lowly_expressed" in GTEX_data) was found to be testis-specific
when multi-mapped reads were counted for gene expression in
normal tissues ("not_analysed" or "testis_specific") (see
?normal_tissues_multimapping_data for details).
Column HPA_RNA_single_cell_type_specific_nTPM specifies the cell types in
which genes were detected in the HPA single cell data (see
?HPA_cell_type_specificity for details).
Column max_HPA_germcell specifies if the maximum expression value in a
germ cell type. (see ?HPA_cell_type_specificity for details).
Column max_HPA_somatic specifies if the maximum expression value in a
somatic cell type. (see ?HPA_cell_type_specificity for details).
Column not_detected_in_somatic_HPA specifies if the gene is detected or
not in a somatic cell type. (see ?HPA_cell_type_specificity for details).
Column HPA_ratio_germ_som gives the ratio between max_HPA_germcell and
max_HPA_somatic columns.
Column percent_of_positive_CCLE_cell_lines gives the percentage
of CCLE cancer cell lines in which genes are expressed (genes
were considered as expressed if TPM >= 1).
Column percent_of_negative_CCLE_cell_lines gives the percentage
of CCLE cancer cell lines in which genes are repressed (TPM <=
0.5).
Column max_TPM_in_CCLE gives the highest expression level of
genes in CCLE cell lines.
Column CCLE_category gives the category assigned to each gene
using CCLE data. "Activated" category corresponds to genes
expressed in at least 1% of cell lines (TPM >= 1) and repressed in
at least 20% of cell lines.
Column percent_pos_tum gives the percentage of TCGA cancer
samples in which genes are expressed (genes were considered as
expressed if TPM >= 1).
Column percent_neg_tum gives the percentage of TCGA cancer samples in
which genes are repressed (TPM <= 0.5).
Column max_TPM_in_TCGA gives the highest expression level of
genes in TCGA cancer sample.
Column max_q75_in_NT gives the maximum q75 expression in normal
peritumoral tissues from TCGA.
Column TCGA_category gives the category assigned to each gene
using TCGA data. "activated" category corresponds to genes
expressed in at least 1% of tumors (TPM >= 1) and repressed in at
least 20% of samples. "multimapping_issue" corresponds to genes
that need multi-mapping to be allowed in order to be analysed
properly.
Columns external_transcript_name, ensembl_transcript_id, and
transcript_biotype give the references and informations about
the most biologically relevant transcript associated to each
gene.
Column IGV_backbone indicates if a gene has been removed from CT genes
as RNA-Seq reads were not properly aligned on exons, but were instead
spread across a wide genomic region spanning the genes.
Column family gives the gene family name.
Column DAC_induced summarises the results (TRUE or FALSE)
of a differential expression evaluating gene induction upon DAC
treatment in a series of cell lines.
Column named CpG_density, gives the density of CpG within each
promoter (number of CpG / promoter length * 100).
Column CpG_promoter classifies the promoters according to their
CpG densities: "low" (CpG_density < 2), "intermediate"
(CpG_density >= 2 & CpG_density < 4), and "high" (CpG_density >=
4).
Column somatic_met_level that gives the mean methylation level
of each promoter in somatic tissues.
Column sperm_met_level that gives the methylation level of each
promoter in sperm.
Column somatic_methylation indicates if the promoter's mean
methylation level in somatic tissues is higher than 50%.
Column germline_methylationindicates if the promoter is
methylated in germline, based on the ratio with somatic tissues
(FALSE if somatic_met_level is at least twice higher than
germline_met_level).
Columns oncogene and tumor_suppressor informs if oncogenic
and tumor-suppressor functions have been associated to genes
(source: Cancermine).
See scripts/make_all_genes_prelim.R and
scripts/make_all_genes_and_CT_genes.Rfor details on how this list of
curated CT genes was created.
DEPRECATED after v1.5, see mean_methylation_in_tissues
Mean methylation values of all CpGs located within Cancer-Testis
(CT) promoters in a set of normal tissues
A SummarizedExperiment object with 298 rows and 14 columns
Rows correspond to CT genes
Mean methylation levels in normal tissues are stored in columns
CpG densities and results of methylation analysis are stored in rowData
The rowData contains:
A column named CpG_density, gives the density of CpG within
each promoter (number of CpG / promoter length * 100).
A column CpG_promoter that classifies the promoters according
to their CpG densities: "low" (CpG_density < 2), "intermediate"
(CpG_density >= 2 & CpG_density < 4), and "high" (CpG_density >=
4).
A column somatic_met_level that gives the mean methylation
level of each promoter in somatic tissues.
A column sperm_met_level that gives the methylation level of
each promoter in sperm.
A column somatic_methylation indicates if the promoter's mean
methylation level in somatic tissues is higher than 50%.
A column germline_methylationindicates if the promoter is
methylated in germline, based on the ratio with somatic tissues
(FALSE if somatic_met_level is at least twice higher than
germline_met_level).
WGBS methylation data was downloaded from Encode and from GEO
databases. Mean methylation levels are evaluated using methylation
values of CpGs located in promoter region (defined as 1000 nt
upstream TSS and 200 nt downstream TSS) (see
scripts/make_CT_mean_methylation_in_tissues.R for details).
DEPRECATED after v1.5, see methylation_in_tissues
Methylation values of CpGs located within Cancer-Testis (CT)
promoters in a set of normal tissues.
A RangedSummarizedExperiment object with 51725 rows and 14 columns
Rows correspond to CpGs (located within CT genes promoters)
Columns correspond to normal tissues
Methylation values from WGBS data
rowRanges correspond to CpG positions
WGBS methylation data was downloaded from Encode and from GEO
databases (see scripts/make_CT_methylation_in_tissues.R for
details).
This is the companion Package for CTexploreR containing omics
data to select and characterise CT genes.
Data come from public databases and include expression and methylation values of genes in normal and tumor samples as well as in tumor cell lines, and expression in cells treated with a demethylating agent is also available.
The CTdata() function returns a data.frame with all the
annotated datasets provided in the package. For details on these
individual datasets, refer to their respective manual pages.
See the vignette and the respective manuals pages for more details about the package and the data themselves.
CTdata()CTdata()
A data.frame describing the data available in
CTdata.
Laurent Gatto
CTdata()CTdata()
Gene expression values in a set of cell lines treated or not with 5-Aza-2'-Deoxycytidine (DAC), a demethylating agent.
A SummarizedExperiment object with 24516 rows and 32 columns
Rows correspond to genes (ensembl_gene_id).
Columns correspond to samples.
Expression data correspond to counts that have been normalised (by DESeq2 method) and log-transformed (log1p).
The colData contains the SRA references of the fastq files that were downloaded, and informations about the cell lines and the DAC treatment.
The rowData contains the results of a differential expression
evaluating the DAC treatment effect. For each each cell line, the
log2FC between treated and control cells is given, as well as the
p-adjusted value. The column induced flags genes significantly
induced (log2FoldChange >= 2 and padj <= 0.1) in at least one
cell line. The threshold is not too stringent as DAC is expected to induce
low expression levels (demethylation doesn't necessarily occurs in
all treated cells...).
When all cells lines already express the gene before DAC treatment, no
assessment of induction was done.
Differential expression analysis was done using DESeq2_1.36.0,
using as design = ~ treatment (see
scripts/make_DAC_treated_cells.R for details).
RNAseq
fastq files were downloaded from Encode database. SRA reference of samples are stored in the colData.
Gene expression values in a set of cell lines treated or not with 5-Aza-2'-Deoxycytidine (DAC), a demethylating agent. Many CT genes belong to gene families from which members have identical or nearly identical sequences. Some CT can only be detected in RNAseq data in which multimapping reads are not discarded.
A SummarizedExperiment object with 24516 rows and 32 columns
Rows correspond to genes (ensembl_gene_id).
Columns correspond to samples.
Expression data correspond to counts that have been normalised (by DESeq2 method) and log-transformed (log1p).
The colData contains the SRA references of the fastq files that were downloaded, and informations about the cell lines and the DAC treatment.
The rowData contains the results of a differential expression
evaluating the DAC treatment effect. For each each cell line, the
log2FC between treated and control cells is given, as well as the
p-adjusted value. The column induced flags genes significantly
induced (log2FoldChange >= 2 and padj <= 0.1) in at least one
cell line. The threshold is not too stringent as DAC is expected to induce
low expression levels (demethylation doesn't necessarily occurs in
all treated cells...).
When all cells lines already express the gene before DAC treatment, no
assessment of induction was done.
Differential expression analysis was done using DESeq2_1.36.0,
using as design = ~ treatment (see
scripts/make_DAC_treated_cells_multimapping.R for details).
RNAseq fastq files were downloaded from Encode database. SRA reference of samples are stored in the colData.
Human embryo single cell RNAseq data in RPKM from
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos (Petropulous et al, 2014)
A SingleCellExperiment object with 26178 rows and 1481 columns
Rows correspond to genes (gene names as rownames)
Columns correspond to cells
Description of the colData:
Column individual gives the sample the cell is coming from.
Column stage specifies the stage of the early embryo.
Column sex is the sex inference made using the expression of 11
Y-linked genes, made for each day individually.
Column ambigous indicates if the inference of the embryo's sex was
ambigous due to some cells expression of the Y-linked genes.
RPKM and metadata files were downloaded from
https://www.ebi.ac.uk/biostudies/files/E-MTAB-3929/
The data were converted in a SingleCellExperiment
(see scripts/make_embryo_sce_Petropoulos.R for details).
Human embryo single cell RNAseq data in FPKM from
Single Cell DNA Methylome Sequencing of Human Preimplantation Embryos (Zhu et al. 2018)
A SingleCellExperiment object with 26255 rows and 50 columns
Rows correspond to genes (gene names as rownames)
Columns correspond to cells
Description of the colData:
Column embryo gives the embryo the cell is coming from.
Column stage specifies the stage of the early embryo.
Column sex is the sex inference made using the expression of RPS4Y1. If
mean expression of RPS4Y1 is higher than 50 FPKM, the sample is male.
50 FPKM files were downloaded from GEO
(accession: GSE81233). The data were converted in a SingleCellExperiment
(see scripts/make_embryo_sce_Zhu.R for details).
Human fetal gonad single cell RNAseq data from
Single-cell roadmap of human gonadal development
(Garcia-Alonso, Nature 2022)
A SingleCellExperiment object with 22489 rows and 10850 columns
Rows correspond to genes (gene names as rownames)
Columns correspond to cells
Description of the colData:
Column type gives the gender and the cell type.
Column stage specifies if the cell type is "pre-meiotic" or "meiotic".
Column germcell is set to TRUE when the cell type is a germ cell.
ee58527e-e1e4-465d-8dc8-800ee40f14f2.rds file dowloaded from
https://cellxgene.cziscience.com/collections/661a402a-2a5a-4c71-9b05-b346c57bc451Data.
The data were converted in a SingleCellExperiment
(see scripts/make_FGC_sce.R for details).
Gene expression data in normal tissues from GTEx database.
A SummarizedExperiment object with 24504 rows and 32 columns
Rows correspond to genes (ensembl_gene_id as rownames)
Columns correspond to tissues
Expression data from the assay are TPM values
The rowData contains
A column named GTEX_category, specifying the tissue specificity
category ("testis_specific", "testis-preferential",
"lowly_expressed" or "other") assigned to each gene using
expression values in testis and in somatic tissues, has been
added to the rowData. "testis_specific" genes are expressed
exclusively in testis (expression in testis >= 1 TPM, highest
expression in somatic tissues < 0.5 TPM, and expressed at least
10x more in testis than in any somatic
tissue). "testis-preferential" genes are genes expressed in
testis but also in a few somatic tissues (expression in testis >=
1 TPM, and allowed in a minority of somatic tissues
(q75_TPM_somatic < 0.5) and expressed at least 10x more in testis than in
any somatic tissue). "lowly_expressed" genes are genes undetectable in GTEX
database probably due to multi-mapping issues (expression in all
GTEX tissues < 1 TPM).
A column named q75_TPM_somatic giving the quantile 75% of TPM
in a somatic tissue.
A column named max_TPM_somatic giving the maximum expression
level found in a somatic tissue.
A column named ratio_testis_somatic giving the ratio between the TPM
in testis and the max TPM in a somatic tissue
Downloaded from
https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz.
Some categories of tissues were pooled (mean expression values are
given in pooled tissues) (see scripts/make_GTEX_data.R for
details).
Gene expression data in human embryonic stem cells
A SummarizedExperiment object with 24488 rows and 4 columns
Rows correspond to genes (ensembl_gene_id as rownames)
Columns correspond to hESC types
Expression data from the assay are TPM values
The colData contains
Column genotype gives the sexual genotype of the cells
RNAseq fastq files were downloaded from Encode databas (see
scripts/make_hESC_data.R for details).
Cell type specificities based on scRNAseq data from the Human Protein Atlas (https://www.proteinatlas.org)
A tibble object with 24504 rows and 7 columns.
Rows correspond to genes (ensembl_gene_id)
Columns give genes cell type specificities
Column HPA_scRNAseq_celltype_specific_nTPM gives the cell types in
which genes were detected (corresponds to column
RNA single cell type specific nTPM of proteinatlas.tsv file.
Column max_HPA_germcell specifies if the maximum expression value in a
germ cell type
Column max_HPA_somatic specifies if the maximum expression value in a
somatic cell type
Column not_detected_in_somatic_HPA specifies if the gene is detected or
not in a somatic cell type. Genes are flagged as
TRUE if the max_HPA_somatic value is equal to 0, and FALSE if
max_HPA_somatic value is > 0. NA is set when the original table from HPA
had no values for that gene.
Column HPA_ratio_germ_som gives the ratio between max_HPA_germcell and
max_HPA_somatic columns.
proteinatlas.tsv was downloaded from the Human Protein Atlas
(https://www.proteinatlas.org)
See scripts/make_HPA_cell_type_specificities.R for details.
A short function that returns the default CTdata tags and, if provided, additional data-specific tags.
makeTags(x)makeTags(x)
x |
An optional |
A character containing the default tags and optional
data-specific tags. If x is missing or is of length 0, the
default tags are returned. Otherwise, a vector of length equal to
length(x) is returned.
CTdata:::makeTags() ## only default tags CTdata:::makeTags(character()) ## only default tags CTdata:::makeTags("myTag") ## one additional tag CTdata:::makeTags(c("myTag", "myOtherTag")) ## two additional tagCTdata:::makeTags() ## only default tags CTdata:::makeTags(character()) ## only default tags CTdata:::makeTags("myTag") ## one additional tag CTdata:::makeTags(c("myTag", "myOtherTag")) ## two additional tag
Mean methylation values of all CpGs located within all genes
promoters in early embryos. Data is based on hg19 reference genome ! From
Single Cell DNA Methylome Sequencing of Human Preimplantation Embryos (Zhu et al. 2018)
A RangedSummarizedExperiment object with 24441 rows and 492 columns
Rows correspond to all genes (gene names as rownames)
Mean methylation levels in embryos types are stored in columns
rowRanges correspond to the hg19 promoter positions
The rowData contains:
A column named ensembl_gene_id containing gene ids.
WGBS methylation data was downloaded from GEO. Mean methylation levels are
evaluated using methylation values of CpGs located in promoter region
(defined as 1000 nt upstream TSS and 500 nt downstream TSS) (see
scripts/make_mean_methylation_in_embryos.R for details).
Mean methylation values of all CpGs located within all genes
promoters in fetal germ cells. Data is based on hg19 reference genome ! From
Dissecting the epigenomic dynamics of human fetal germ cell development at single-cell resolution (Li et al. 2021)
A RangedSummarizedExperiment object with 24441 rows and 337 columns
Rows correspond to all genes (gene names as rownames)
Mean methylation levels in FGC types are stored in columns
rowRanges correspond to the hg19 promoter positions
The rowData contains:
A column named ensembl_gene_id containing gene ids.
WGBS methylation data was downloaded from GEO. Mean methylation levels are
evaluated using methylation values of CpGs located in promoter region
(defined as 1000 nt upstream TSS and 500 nt downstream TSS) (see
scripts/make_mean_methylation_in_FGC.R for details).
Mean methylation values of all CpGs located within all genes promoters in human embryonic stem cells
A SummarizedExperiment object with 24488 rows and 3 columns
Rows correspond to all genes (gene names as rownames)
Mean methylation levels in hESC types are stored in columns
The rowData contains:
A column named ensembl_gene_id containing gene ids.
The colData contains
Column genotype gives the sexual genotype of the cells
WGBS methylation data was downloaded from Encode. Mean methylation levels are
evaluated using methylation values of CpGs located in promoter region
(defined as 1000 nt upstream TSS and 200 nt downstream TSS) (see
scripts/make_mean_methylation_in_hESC.R for details).
Mean methylation values of all CpGs located within all genes promoters in a set of normal tissues
A SummarizedExperiment object with 24502 rows and 14 columns
Rows correspond to all genes (gene names as rownames)
Mean methylation levels in normal tissues are stored in columns
CpG densities and results of methylation analysis are stored in rowData
The rowData contains:
A column named CpG_density, gives the density of CpG within
each promoter (number of CpG / promoter length * 100).
A column CpG_promoter that classifies the promoters according
to their CpG densities: "low" (CpG_density < 2), "intermediate"
(CpG_density >= 2 & CpG_density < 4), and "high" (CpG_density >=
4).
A column somatic_met_level that gives the mean methylation
level of each promoter in somatic tissues.
A column sperm_met_level that gives the methylation level of
each promoter in sperm.
A column somatic_methylation indicates if the promoter's mean
methylation level in somatic tissues is higher than 50%.
A column germline_methylationindicates if the promoter is
methylated in germline, based on the ratio with somatic tissues
(FALSE if somatic_met_level is at least twice higher than
germline_met_level).
WGBS methylation data was downloaded from Encode and from GEO
databases. Mean methylation levels are evaluated using methylation
values of CpGs located in promoter region (defined as 1000 nt
upstream TSS and 200 nt downstream TSS) (see
scripts/make_mean_methylation_in_tissues.R for details).
Methylation values of CpGs located within all genes
promoters in embryo. Data is based on hg19 reference genome ! From
Single Cell DNA Methylome Sequencing of Human Preimplantation Embryos (Zhu et al. 2018)
A RangedSummarizedExperiment object with 1915545 rows and 492 columns
Rows correspond to CpGs (located within all genes promoters (TSS +- 1000 nt))
Columns correspond to cells
Methylation values from scWGBS data
rowRanges correspond to CpG positions
Description of the colData:
Column cell_type indicates the embryo type.
Column bulk_or_single_cell specifies if the sample was indeed only a
single cell or a bulk of several cells.
Other information about the sequencing of each sample are clearly labelled
scWGBS methylation data was downloaded from GEO database
(see scripts/make_methylation_in_embryo.R for details).
Methylation values of CpGs located within all genes
promoters in fetal germ cells. Data is based on hg19 reference genome ! From
Dissecting the epigenomic dynamics of human fetal germ cell development at single-cell resolution (Li et al. 2021)
A RangedSummarizedExperiment object with 1915545 rows and 337 columns
Rows correspond to CpGs (located within all genes promoters (TSS +- 1000 nt))
Columns correspond to cells
Methylation values from scWGBS data
rowRanges correspond to CpG positions
Description of the colData:
Column type indicates if the cell type is somatic or FGC
Column time_week specifies the time of the embryo when cells were removed.
Column sex indicates the sex of the cells.
Other information about the sequencing of each sample are clearly labelled
scWGBS methylation data was downloaded from GEO database
(see scripts/make_methylation_in_FGC.R for details).
Methylation values of CpGs located within all genes promoters in human embryonic stem cells.
A RangedSummarizedExperiment object with 4280098 rows and 3 columns
Rows correspond to CpGs (located within all genes promoters (TSS +- 5000 nt))
Columns correspond to hESC
Methylation values from WGBS data
rowRanges correspond to CpG positions
WGBS methylation data was downloaded from Encode
(see scripts/make_methylation_in_hESC.R for details).
Methylation values of CpGs located within all genes promoters in a set of normal tissues.
A RangedSummarizedExperiment object with 4280327 rows and 14 columns
Rows correspond to CpGs (located within all genes promoters (TSS +- 5000 nt))
Columns correspond to normal tissues
Methylation values from WGBS data
rowRanges correspond to CpG positions
WGBS methylation data was downloaded from Encode and from GEO
databases (see scripts/make_methylation_in_tissues.R for
details).
Gene expression values (TPM) in a set of normal tissues obtained by counting or not multi-mapped reads. Many CT genes belong to gene families from which members have identical or nearly identical sequences. Some CT can only be detected in RNAseq data in which multimapping reads are not discarded.
A SummarizedExperiment object with 24504 rows and 18 columns
Rows correspond to genes (ensembl_gene_id)
Columns correspond to normal tissues.
First assay, TPM_no_multimapping, gives TPM expression values
obtained when discarding multimapped reads.
Second assay, TPM_with_multimapping, gives TPM expression
values obtained by counting multimapped reads.
A column named multimapping_analysis has been added to the
rowData. It summarizes the testis specificity analysis of genes
flagged as "lowly_expressed" in GTEX_data. Genes are considered
"testis_specific" when, with multimapping allowed, they are
detectable in testis (TPM >= 1), their TPM value has increased
compared to without multimapping (ratio > 5), and their TPM value
is at least 10 times higher in testis than in any other somatic
tissue (where the maximum expression always has to be below 1 TPM).
Genes are considered "testis_preferential" when, with multimapping allowed,
they are detectable in testis (TPM >= 1), their TPM value has increased
compared to without multimapping (ratio > 5), and their TPM value
is at least 10 times higher in testis than in any other somatic
tissue (where the maximum expression is above 1 TPM).
RNAseq fastq files were downloaded from Encode database (see
scripts/make_normal_tissues_multimapping.R for details).
Human oocytes single cell RNAseq data from
Decoding dynamic epigenetic landscapes in human oocytes using single-cell multi-omics sequencing (Yan et al. Cell Stem Cell 2021)
A SingleCellExperiment object with 26500 rows and 899 columns
Rows correspond to genes(gene names as rownames)
Columns correspond to cells
Description of the colData:
Column type gives the cell type.
Column stage specifies if the cell type is "pre-meiotic" or "meiotic".
Column germcell is set to TRUE when the cell type is a germ cell.
GSE154762_hO_scChaRM_count_matix.txt.gzwas downloaded from GEO (accession: GSE154762). The data were converted in a SingleCellExperiment (seescripts/make_oocytes_sce.R' for details).
Gene expression profiles in different human cell types based on scRNAseq data obtained from the Human Protein Atlas (https://www.proteinatlas.org)
A SingleCellExperiment object with 20082 rows and 66 columns
Rows correspond to genes (ensembl gene id as rownames)
Columns correspond to cell types
Expression values correspond to transcripts per million protein coding genes (pTPM)
Description of the colData:
Column Cell_type gives cell type.
Column group gives the cell type group (defined in the Human Protein Atlas).
Description of the rowData:
Column max_TPM_in_a_somatic_cell_type gives the maximum expression value
found in a somatic cell type
Column max_in_germcells_group gives the maximum expression value found
in a germ cell type
Column Higher_in_somatic_cell_type specifies if a somatic cell type
Gene expression values in cell types, based on multiple scRNAseq datasets
obtained from the Human Protein Atlas
(https://www.proteinatlas.org/about/download)
The data were converted in a SummarizedExperiment
(see scripts/14_make_scRNAseq_HPA.R for details).
DEPRECATED after v1.5, see TCGA_methylation
Methylation values of probes located within Cancer-Testis (CT)
promoters in samples from TCGA (tumor and peritumoral samples)
A RangedSummarizedExperiment object with 666 rows and 3423
columns
Rows correspond to Infinium 450k probes
Columns correspond to samples
Methylation data from the assay are Beta values
Clinical information are stored in colData
Probe information (hg38 coordinates) are stored in rowRanges
SKCM, LUAD, LUSC, COAD, ESCA, BRCA and HNSC methylation data were
downloaded with TCGAbiolinks and subsetted to select probes located
in CT genes promoter regions (see
scripts/make_TCGA_CT_methylation.R for details).
Methylation values of probes located within all genes promoters in samples from TCGA (tumor and peritumoral samples)
A RangedSummarizedExperiment object with 79445 rows and 3423
columns
Rows correspond to Infinium 450k probes
Columns correspond to samples
Methylation data from the assay are Beta values
Clinical information are stored in colData
Probe information (hg38 coordinates) are stored in rowRanges
SKCM, LUAD, LUSC, COAD, ESCA, BRCA and HNSC methylation data were
downloaded with TCGAbiolinks and subsetted to select probes located
in CT genes promoter regions (see
scripts/make_TCGA_methylation.R for details).
Gene expression data in TCGA samples (tumor and peritumoral samples).
A SummarizedExperiment object with 24497 rows and 4141 columns
Rows correspond to genes (ensembl_gene_id)
Columns correspond to samples
Expression data from the assay are TPM values
Clinical information are stored in colData
Genes information are stored in rowData
The colData contains clinical data from TCGA as well as global
hypomethylation levels obtained from paper DNA methylation loss
promotes immune evasion of tumours with high mutation and copy
number load from Jang et al., Nature Commun 2019 that were added
(see inst/scripts/make_TCGA_TPM.R for details).
The rowData contains genes information and, for each gene, the
percentage of tumors that are positive (TPM >= 1), and the
percentage of tumors that are negative (TPM < 0.5). In column
TCGA_category, genes are labelled as "activated" when the
percentage of positive tumors is > 1, with a maximal expression higher than
5 TPM, and when at least 20% of tumors are negative. Genes are labelled as
"not_activated" when the percentage of positive tumors is lower than 1.
Genes are labelled as "leaky" when less than 20% of tumors are negative.
Genes are labelled as "lowly_expressed" when repressed (TPM <= 0.5)
in at least 20%, expressed (TPM >= 1) in more than 1 % of cell lines, with
a maximum expression lower than 5 TPM.
SKCM, LUAD, LUSC, COAD, ESCA, BRCA and HNSC expression data were
downloaded with TCGAbiolinks (see scripts/make_TCGA_TPM.R
for details).
Testis single cell RNAseq data from
The adult human testis transcriptional cell atlas (Guo et al. 2018)
A SingleCellExperiment object with 20891 rows and 6490 columns
Rows correspond to genes (gene names as rownames)
Columns correspond to testis cells
Description of the colData:
Column nGene gives the number of distinct genes detected per cell.
Column nUMI gives the total UMI number per cell.
Column clusters gives cluster number defined in the Guo's paper.
Column type gives the testis cell type associated to the cluster number.
Column Donor gives the Donor origin of the cells.
Description of the rowData:
Column percent_pos_testis_germcells gives the percent of testis germ cells
in wich the genes are detected (count > 0) (based on testis scRNAseq data).
Column percent_pos_testis_somatic gives the percent of testis somatic cells
in wich the genes are detected (count > 0) (based on testis scRNAseq data).
Columntestis_cell_type specifies the testis cell-type showing the highest
mean expression of each gene (based on testis scRNAseq data).
The rowData contains the testis_cell_type column, specifying the testis
cell-type showing the highest mean expression of each gene.
The count matrix GSE112013_Combined_UMI_table.txt.gz was downloaded from
GEO (accession: GSE112013). Metadata correspond to TableS1 from the paper's
supplemental data. The data were converted in a SingleCellExperiment
(see scripts/13_make_testis_sce.R for details).