MeDeMo - a dependency model for DNA methylation-aware transcription factor binding predictions
Authors/Creators
- 1. Institute of Computer Science, Martin Luther University Halle-Wittenberg
- 2. Computational Epigenomics and Systems Cardiology, Zentrum f\"ur Molekulare Medizin G\"othe Universit\"at
- 3. Systems Biology and Data Analytics, Genome Institute of Singapore
Description
The uploaded fasta files contain extended reference genomes for three cell lines HepG2, GM12878, K562 (ENCODE) and two primary liver hepatocyte samples from the german epigenomics consortium (DEEP). The extended reference genomes contain information on DNA methylation in a CpG context. They can be used as input for MeDeMo, a tool to infer transcription factor binding sites incorporating not only sequence specificity but also DNA methylation. MeDeMo is available online at: http://www.jstacs.de/index.php/MeDeMo.
We considered the files ENCFF279HCL and ENCFF835NTC for GM12878, ENCFF867JRG and ENCFF721JMB for K562 as well as ENCFF064GJQ and ENCFF369YQW for HepG2. From DEEP, we considered samples 41_Hf01 and 41_Hf03 which are available through the International Human Epigenomics Consortium (IHEC).
In addition, we provide all models trained using the mentioned data sets.
Files
Files
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