Persistent Identifier
|
doi:10.11588/data/RDISCE |
Publication Date
|
2022-03-07 |
Title
| Prediction and Comparative Analysis of CTCF Binding Sites based on a First Principle Approach [Research Data] |
Author
| Li, Kunhe (Institute for Theoretical Physics, Heidelberg University, Germany)
Oiwa, Nestor Norio (Universidade Federal Fluminense, Brazil)
Cordeiro, Claudette E. (Universidade Federal Fluminense, Brazil)
Heermann, Dieter W. (Institute for Theoretical Physics, Heidelberg University, Germany) |
Point of Contact
|
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Li, Kunhe (Institute for Theoretical Physics, Heidelberg University, Germany)
Oiwa, Nestor Norio (Universidade Federal Fluminense, Brazil)
Cordeiro, Claudette E. (Universidade Federal Fluminense, Brazil)
Heermann, Dieter W. (Institute for Theoretical Physics, Heidelberg University, Germany) |
Description
| The file contains the CTCF-DNA binding sites for complete genome of Homo sapiens (human), Mus musculus (mouse), Sus scrofa (pig), Capra hircus (goat), Aedes aegypti (dengue and yellow fever mosquito) and Drosophila melanogaster (fruit fly) using electronic nucleotide alignment. The data analysis is described in NN Oiwa, K Li, CE Cordeiro and DW Heermann, 2022 [arXiv:2110.10508]. Detailed description of the Electronic Nucleotide Alignment method can be found in NN Oiwa, CE Cordeiro, DW Heerman (2016). We also add Caenorhabditis elegans (worm), Plasmodium falciparum (protozoan) and Arabidopsis thaliana (plant) as negative test, since there is not CTCF in these species. (2022-02-08) |
Subject
| Computer and Information Science; Medicine, Health and Life Sciences; Physics |
Keyword
| CTCF
zinc finger
extended ladder model |
Topic Classification
| genetics
statistical physics
bioinformatics |
Related Publication
| Oiwa, N. N., Li, K., Cordeiro, C. E., & Heermann, D. W. (2022). Prediction and comparative analysis of CTCF binding sites based on a first principle approach. Physical Biology, 19(3), 036005. doi: https://doi.org/10.1088/1478-3975/ac5dca https://doi.org/10.1088/1478-3975/ac5dca
Nestor Norio Oiwa, Kunhe Li, Claudette E. Cordeiro and Dieter W. Heermann (2022). Prediction and Comparative Analysis of CTCF Binding Sites based on a First Principle Approach. arXiv: 2110.10508 https://arxiv.org/abs/2110.10508 |
Funding Information
| Conselho Nacional de Desenvolvimento Tecnologico e Cientifico (CNPq), Brazil: 248589/2013
bwHPC, Baden-Wuerttemberg
German Research Foundation (DFG): INST 35/1134-1 FUGG
Chinese Scholarship Council
Deutsche Forschungsgemeinschaft (DFG, German Research Foundation): EXC 2181/1 - 390900948 |
Deposit Date
| 2021-10-22 |