Caine Lucas Grandt, Lara Kim Brackmann, Alicia Poplawski, Heike Schwarz, Federico Marini, Thomas Hankeln, Danuta Galetzka, Sebastian Zahnreich, Johanna Mirsch, Claudia Spix, Maria Blettner, Heinz Schmidberger, Manuela Marron
Identification of lncRNAs involved in response to ionizing radiation in fibroblasts of long-term survivors of childhood cancer and cancer cancer-free controls: the KiKme Study
The files of this repository (https://github.com/clg1990/KiKme_lncRNA) are intended to be used in chronological order (1-4). They are built according to the instruction of the WGCNA package (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-559). The mRNA-Seq and lncRNA-Seq data and associated meta data are not publicly available due to data protection regulations of the KiKme-study. All results created using the pipeline will be added with the release of the preprint/accepted manuscript.
- Merging and clustering of mRNA- and lncRNA-Seq data, analysis for outliers, creation of trait data
- Construction of the WGCNA-network
- Correlation of trait data with the gene sets (modules) and adjustment of p-values
- Extraction of network-data (adjacency, connectivity, etc.)