Zieger_et al_Modified denovoLOBGOB pipeline

This is a modified version of denovoLOBGOB¹ to analyze transcription factor binding sites at regions of de novo mutations using position weight matrices from JASPAR 2020².

This Zenodo repository contains R-Scripts for the analysis of transcription factor binding sites in datasets of de novo mutations (DNMs) which have been used for the analysis of DNMs in whole genome sequencing data (WGS) of trios with nonsyndromic cleft lip with or without cleft palate (nsCL/P)³. These R scripts are a modified version from denovoLOBGOB, previously denoted as denovoTF, original code available at GitHub: https://github.com/pjshort/denovoTF.

¹ https://github.com/pjshort/denovoTF/blob/master/scripts/denovoLOBGOB.R
denovoLOBGOB was used for Short et al., 2018
Short, P. J., McRae, J. F., Gallone, G., Sifrim, A., Won, H., Geschwind, D. H., Wright, C. F., Firth, H. V, FitzPatrick, D. R., Barrett, J. C., & Hurles, M. E. (2018). De novo mutations in regulatory elements in neurodevelopmental disorders. Nature, 555(7698), 611–616. https://doi.org/10.1038/nature25983

² https://bioconductor.org/packages/release/data/annotation/html/JASPAR2020.html
Fornes, O., Castro-Mondragon, J.A., Khan, A., van der Lee, R., Zhang, X., Richmond, P.A., Modi, B.P., Correard, S., Gheorghe, M., Baranašić, D., et al. (2019). JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 48, D87–D92.

³ Zieger, H.K., Weinhold, L., Schmidt, A., Holtgrewe, M., Juranek, S.A., Siewert, A., Scheer, A.B., Thieme, F., Mangold, E., Ishorst, N., Brand, F.U., Welzenbach, J., Beule, D., Paeschke, K., Krawitz, P.M. & Ludwig, K.U., Prioritization of non-coding elements involved in non-syndromic cleft lip with/without cleft palate through genome-wide analysis of de novo mutations, HGG Adv.