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Dataset . 2020
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ZENODO
Dataset . 2020
License: CC BY
Data sources: ZENODO
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ZENODO
Dataset . 2020
License: CC BY
Data sources: Datacite
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ZENODO
Dataset . 2020
License: CC BY
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ZENODO
Dataset . 2020
License: CC BY
Data sources: ZENODO
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MeDeMo - a dependency model for DNA methylation-aware transcription factor binding predictions

Research datakeyboard_double_arrow_right Dataset 23 Mar 2020Publisher:Zenodo
Authors: Grau, Jan; Schulz, Marcel; Schmidt, Florian;

doi: 10.5281/zenodo.3723985 , 10.5281/zenodo.3723984 , 10.5281/zenodo.6274622

MeDeMo - a dependency model for DNA methylation-aware transcription factor binding predictions

Abstract

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.

Related Organizations
Keywords

DNA methylation, fasta, TF binding, Genomic sequence

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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