Curated list of genes reported in the literature as up- or down-regulated when monocytes differentiate in vitro into monocyte-derived dendritic cells (moDCs), grouped by biological process. Used to check the expected transcriptional changes (Figure 4C of the article).
Format
A data frame with 90 rows and 7 columns:
- gene
Gene symbol.
- Gene_name
Name used in the source publication (e.g.,
"IL-1beta").- process
Biological process (e.g.,
"Maturation","Cytokines").- Associated_pathways
Pathway or description reported in the source.
- Expression
Reported direction:
UpregulatedorDownregulated.- link
Link to the source publication.
- contrast
Comparison in which the change was reported.
Details
The script that generates it is data-raw/lesson5_data.R.
Text was converted to ASCII (Greek letters spelled out) and the spreadsheet
artifact "GBP 2.00" was corrected to "GBP2".
Eleven entries use aliases or old names (CD31, CD54,
IL8, IRF7A, ERF2, CD32, TNFR2,
IP3KB, HSP27, GRP78) or genes absent from the
data (CXCL8); they do not match the gene symbols of
filtered_txi and, as in the original analysis, are not shown.
Examples
table(moDC_genes$process)
#>
#> Adenosine receptors
#> 2
#> Antigen processing and presentation
#> 4
#> Ca2+ binding
#> 2
#> Cell adhesion and motility
#> 6
#> Chemokines
#> 4
#> Cytokines
#> 11
#> Growth factors
#> 2
#> Immune regulation
#> 2
#> Lipid metabolism
#> 6
#> Maturation
#> 7
#> Pattern and antigen recognition
#> 3
#> Regulatory
#> 6
#> Signal transduction/Growth control
#> 4
#> Signaling molecules
#> 6
#> TP53 Regulates Transcription of Cell Death Genes
#> 1
#> Th2 response
#> 10
#> Transcription factors
#> 3
#> Transcription regulation
#> 7
#> chaperones
#> 2
#> oxidative stress
#> 2