Analysis of DEPDC5 KO transcriptome data

The here provided code and output data is accompanying information for the following research article

The transcriptomic signature of DEPDC5 KO induced mTOR-hyperactivation in human neurons and its response to rapamycin treatment Mattson S. O. Jones^1,2, Regina Waltes¹, Silvia Lindlar¹, Johannes Ludwig¹, Evelyn Ullrich^3,4,5, Dan Geschwind^6,7,8,9, Jasmin Hefendehl^10,11, Karl Martin Klein^12,2,13, Felix Rosenow^12,2, Denise Haslinger¹ and Andreas Geburtig-Chiocchetti^1,2 (shared last)
The manuscript is currently in preparation and will be linked here upon publication; DOI will be provided

All analyses were organized using the workflowr package. The rendered output is available here

Installation guidelines

1. Install R

   • (Recommended) Install RStudio

   • (Recommended) Install pandoc (Instructions)

   • (Recommended) Install Git

2. Install packages

   # installs cran packages
    package<-c("RColorBrewer", "dplyr", "httr", "parallel", "rJava",
            "compareGroups", "kableExtra", "tidyverse","dendextend",
            "knitr", "pheatmap", "glmpca", "plotly", "rsconnect", "openxlsx",
            "lavaan", "semPlot", "ggplotify", "qqman", "webshot", "M3C",
            "data.table")
   
   
   if(length(setdiff(package, rownames(installed.packages()))) > 0)	{
     install.packages(setdiff(package, rownames(installed.packages())),
                      INSTALL_opts = c('--no-lock'),dependencies=T,
                      ask=FALSE, repos="https://cloud.r-project.org/")
   }
   
   # installs BioC packages
   
   if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager", repos="https://cloud.r-project.org/")
   
   bpackage = c( "annotate","biomaRt", "DESeq2", "WGCNA", "edgeR","RRHO",
                 "limma","Rsubread", "flashClust", "gprofiler2", "RCircos",
                 "sva", "vsn", "EnhancedVolcano", "bumphunter",
                 "TxDb.Hsapiens.UCSC.hg19.knownGene", "GenomicRanges", "Gviz",
                 "rtracklayer")
   
   if(length(setdiff(bpackage, rownames(installed.packages()))) > 0)	{
     BiocManager::install(setdiff(bpackage, rownames(installed.packages())))
   }

3. Create an account on GitHub

   • Clone repository (Space needed including generated outputs 4,28 GB)

     git clone https://github.com/KJPMolgenLab/DEPDC5_D62_Analysis.git

   • The code for the statistical analysis can be found in the analysis folder

   • Build the analyses open the R-Project file *DEPDC5_D62_Analysis.Rproj rund worflow command

     wflow_build()

     for more help on working with work_flow we recommend reading the workflow start vignette

Attribution

This work has been funded by the Hessian government (LOEWE Schwerpunkt CePTER)

Affiliations

(DOI will be posted here)

Footnotes

1. Autism Therapy and Research Center of Excellence, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, 60528 Frankfurt am Main, Germany ↩ ↩² ↩³ ↩⁴ ↩⁵ ↩⁶

2. Center for Personalized Translational Epilepsy Research (CePTER), Goethe-University Frankfurt, Frankfurt am Main, Germany ↩ ↩² ↩³ ↩⁴

3. Experimental Immunology, Children's University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany ↩

4. Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt am Main, Germany ↩

5. German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany ↩

6. Program in Neurobehavioral Genetics, Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA ↩

7. Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA ↩

8. Program in Neurogenetics, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA ↩

9. Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA ↩

10. Institute of Cell Biology and Neuroscience, University of Frankfurt, D-60438 Frankfurt am Main, Germany ↩

11. Neurovascular Disorders, Buchmann Institute for Molecular Life Sciences, University of Frankfurt, D-60438 Frankfurt am Main, Germany ↩

12. Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, Goethe-University Frankfurt, Schleusenweg 2-16 (Haus 95), 60528, Frankfurt am Main, Germany ↩ ↩²

13. Departments of Clinical Neurosciences, Medical Genetics, and Community Health Sciences, Hotchkiss Brain Institute & Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada ↩