Last updated: 2021-09-24
Checks: 2 0
Knit directory: femNATCD_MethSeq/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 56bb68f. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: analysis/.Rhistory
Ignored: code/.Rhistory
Ignored: data/Epicounts.csv
Ignored: data/Epimeta.csv
Ignored: data/Epitpm.csv
Ignored: data/KangUnivers.txt
Ignored: data/Kang_DataPreprocessing.RData
Ignored: data/Kang_dataset_genesMod_version2.txt
Ignored: data/PatMeta.csv
Ignored: data/ProcessedData.RData
Ignored: data/RTrawdata/
Ignored: data/SNPCommonFilt.csv
Ignored: data/femNAT_PC20.txt
Ignored: output/BrainMod_Enrichemnt.pdf
Ignored: output/Brain_Module_Heatmap.pdf
Ignored: output/DMR_Results.csv
Ignored: output/GOres.xlsx
Ignored: output/LME_GOplot.pdf
Ignored: output/LME_Results.csv
Ignored: output/LME_Results_Sig.csv
Ignored: output/LME_tophit.svg
Ignored: output/ProcessedData.RData
Ignored: output/RNAvsMETplots.pdf
Ignored: output/Regions_GOplot.pdf
Ignored: output/ResultsgroupComp.txt
Ignored: output/SEM_summary_groupEpi_M15.txt
Ignored: output/SEM_summary_groupEpi_M2.txt
Ignored: output/SEM_summary_groupEpi_M_all.txt
Ignored: output/SEM_summary_groupEpi_TopHit.txt
Ignored: output/SEM_summary_groupEpi_all.txt
Ignored: output/SEMplot_Epi_M15.html
Ignored: output/SEMplot_Epi_M15.png
Ignored: output/SEMplot_Epi_M15_files/
Ignored: output/SEMplot_Epi_M2.html
Ignored: output/SEMplot_Epi_M2.png
Ignored: output/SEMplot_Epi_M2_files/
Ignored: output/SEMplot_Epi_M_all.html
Ignored: output/SEMplot_Epi_M_all.png
Ignored: output/SEMplot_Epi_M_all_files/
Ignored: output/SEMplot_Epi_TopHit.html
Ignored: output/SEMplot_Epi_TopHit.png
Ignored: output/SEMplot_Epi_TopHit_files/
Ignored: output/SEMplot_Epi_all.html
Ignored: output/SEMplot_Epi_all.png
Ignored: output/SEMplot_Epi_all_files/
Ignored: output/barplots.pdf
Ignored: output/circos_DMR_tags.svg
Ignored: output/circos_LME_tags.svg
Ignored: output/clinFact.RData
Ignored: output/dds_filt_analyzed.RData
Ignored: output/designh0.RData
Ignored: output/designh1.RData
Ignored: output/envFact.RData
Ignored: output/functional_Enrichemnt.pdf
Ignored: output/gostres.pdf
Ignored: output/modelFact.RData
Ignored: output/resdmr.RData
Ignored: output/resultsdmr_table.RData
Ignored: output/table1_filtered.Rmd
Ignored: output/table1_filtered.docx
Ignored: output/table1_unfiltered.Rmd
Ignored: output/table1_unfiltered.docx
Ignored: setup_built.R
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made to the R Markdown (analysis/about.Rmd) and HTML (docs/about.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 43333cc | achiocch | 2021-09-24 | adds new build |
| html | b497cc9 | achiocch | 2021-09-17 | Build site. |
| html | ccbc9e4 | achiocch | 2021-08-10 | Build site. |
| html | 70cd649 | achiocch | 2021-08-06 | Build site. |
| html | 2a53a87 | achiocch | 2021-08-06 | Build site. |
| html | e3a9ae3 | achiocch | 2021-08-04 | Build site. |
| html | f6bbdc0 | achiocch | 2021-08-04 | Build site. |
| html | 710904a | achiocch | 2021-08-03 | Build site. |
| html | 16112c3 | achiocch | 2021-08-03 | wflow_publish(c(“analysis/", "code/”, “docs/”)) |
| html | cde8384 | achiocch | 2021-08-03 | Build site. |
| html | d761be4 | achiocch | 2021-07-31 | Build site. |
| html | b452d2f | achiocch | 2021-07-30 | wflow_publish(c(“analysis/", "code/”, "docs/*")) |
| html | 2734c4e | achiocch | 2021-05-08 | Build site. |
| html | a847823 | achiocch | 2021-05-08 | wflow_publish(c(“analysis/", "code/”, "docs/*")) |
| html | 9cc52f7 | achiocch | 2021-05-08 | Build site. |
| html | 158d0b4 | achiocch | 2021-05-08 | wflow_publish(c(“analysis/", "code/”, "docs/*")) |
| html | 0f262d1 | achiocch | 2021-05-07 | Build site. |
| html | 5167b90 | achiocch | 2021-05-07 | wflow_publish(c(“analysis/", "code/”, "docs/*")) |
| html | 05aac7f | achiocch | 2021-04-23 | Build site. |
| html | f5c5265 | achiocch | 2021-04-19 | Build site. |
| html | 17f1eec | achiocch | 2021-04-10 | Build site. |
| html | 91de221 | achiocch | 2021-04-05 | Build site. |
| html | 4ea1bba | achiocch | 2021-02-25 | Build site. |
| html | 6c21638 | achiocch | 2021-02-25 | wflow_publish(c(“analysis/", "code/”, "docs/*"), update = F) |
| Rmd | b10989a | achiocch | 2021-02-25 | Start workflowr project. |
AG Chiocchetti1, A Yousaf1, R Waltes1, A Bernhard1, A Martinelli1, K Ackermann1, D Haslinger1, B Rotter2, N Krezdorn2, K Konrad3,4, G Kohls3, A Vetro5, A Hervas6, A Fernández-Rivas7, CM Freitag1
Corresponding author: Dr. Andreas G. Chiocchetti Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy JW Goethe University Frankfurt Deutschordenstr. 50 60528 Frankfurt am Main Germany mail: andreas.chiocchetti@kgu.de
Keywords: CD, epigenetics, girls, SLITRK5, epigenetic x environment interaction, data integrative analysis
Background: Conduct Disorder (CD) is an impairing psychiatric disorder of childhood and adolescence characterized by aggressive and dissocial behavior. Environmental factors such as maternal smoking during pregnancy, socio-economic status, trauma, or early life stress are associated with CD. Although, the number of female-CD is rising in Western societies, female CD is under-researched. We aimed at exploring the epigenetic signature of female-CD and its relation to psychosocial and environmental risk factors. Methods: We performed HpaII sensitive methylation sequencing of 50 CD girls and 50 matched controls and mixed linear regression models. Identified tags of interest were mapped to brain developmental processes and epigenetic signatures were tested as mediators for risk factors. Results: We identified a 48% increased methylation 5’ of the neurite modulator SLITRK5 (P = 5.47e-07, FDR = 0.142) in cases within a glucocorticoid receptor binding site. Functionally, methylation positively correlated with gene expression in-vitro. At systems-level, hyper-methylated genes (P < 0.05) were associated with development of neocortical regions, thalamus and striatum, whereas hypo-methylated (P < 0.05) genes were enriched with regulators of the steroid hormone system and expressed in amygdala and hippocampus. Mediation of environmental risk, such as adverse parenting conditions and history of trauma on CD status, was specifically observed for differentially methylated genes expressed in the brain developmental networks. Discussion: The differential methylation patterns identified at nominal level of significance in female CD are likely to affect genes that are expressed in brain regions previously indicated in CD. We provide suggestive evidence that the long-term effects of adverse parenting conditions and trauma exposure are likely to be mediated by epigenetic mechanisms impairing specific brain developmental networks and therefore exerting a long-term effect on neural functions in CD. Our results are exploratory and might be biased by false negative and false positive findings. Thus, further replication is needed.