Name
Title | ||
|---|---|---|
Generalizing and learning protein-DNA binding sequence representations by an evolutionary algorithm |
Abstract | ||
|---|---|---|
Protein-DNA bindings are essential activities. Understanding them forms the basis for further deciphering of biological and genetic systems. In particular, the protein-DNA bindings between transcription factors (TFs) and transcription factor binding sites (TFBSs) play a central role in gene transcription. Comprehensive TF-TFBS binding sequence pairs have been found in a recent study. However, they are in one-to-one mappings which cannot fully reflect the many-to-many mappings within the bindings. An evolutionary algorithm is proposed to learn generalized representations (many-to-many mappings) from the TF-TFBS binding sequence pairs (one-to-one mappings). The generalized pairs are shown to be more meaningful than the original TF-TFBS binding sequence pairs. Some representative examples have been analyzed in this study. In particular, it shows that the TF-TFBS binding sequence pairs are not presumably in one-to-one mappings. They can also exhibit many-to-many mappings. The proposed method can help us extract such many-to-many information from the one-to-one TF-TFBS binding sequence pairs found in the previous study, providing further knowledge in understanding the bindings between TFs and TFBSs. |
Year | DOI | Venue |
|---|---|---|
2011 | 10.1007/s00500-011-0692-5 | Soft Comput. |
Keywords | DocType | Volume |
Bioinformatics,Sequence,Protein,DNA,Crowding,Gene transcription,TRANSFAC,PDB | Journal | 15 |
Issue | ISSN | Citations |
8 | 1432-7643 | 9 |
PageRank | References | Authors |
0.55 | 25 | 4 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Ka-Chun Wong | 1 | 291 | 40.18 |
| Chengbin Peng | 2 | 63 | 4.01 |
| Man Hon Wong | 3 | 814 | 233.13 |
| Kwong-Sak Leung | 4 | 1887 | 205.58 |