BinDNase: A discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data

Bioinformatics

Volumn 31, Issue 17, 2015, Pages 2852-2859

  Kähärä, Juhani ^a   Lähdesmäki, Harri ^a  

^a AALTO UNIVERSITY   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN; DEOXYRIBONUCLEASE I; DNA; PROTEIN BINDING; TRANSCRIPTION FACTOR;

ALGORITHM; BINDING SITE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DNA FOOTPRINTING; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; HEPG2 CELL LINE; HIGH THROUGHPUT SEQUENCING; HUMAN; K562 CELL LINE; METABOLISM; PROCEDURES; SOFTWARE;

ALGORITHMS; BINDING SITES; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DEOXYRIBONUCLEASE I; DNA; DNA FOOTPRINTING; GENE EXPRESSION REGULATION; GENOMICS; HEP G2 CELLS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; K562 CELLS; PROTEIN BINDING; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSCRIPTION FACTORS;

EID: 84940734145     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv294     Document Type: Article

References (19)

1. Boyle A.P., et al. (2008). High-resolution mapping, and characterization of open chromatin across the genome. Cell, 132, 311-322
2. Buenrostro J.D., et al. (2013). Transposition of native chromatin for fast, and sensitive epigenomic profiling of open chromatin, dna-binding proteins, and nucleosome position. Nat. Methods, 10, 1213-1218
3. Giresi P.G., et al. (2006). Faire (formaldehyde-assisted isolation of regulatory elements) isolates active regulatory elements from human chromatin. Genome Res., 17, 877-885
4. He H.H., et al. (2014). Refined dnase-seq protocol, and data analysis reveals intrinsic bias in transcription factor footprint identification. Nat. Methods, 11, 73-78
5. John S., et al. (2011). Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat. Genet., 43, 264-268
6. Kasowski M., et al. (2010). Variation in transcription factor binding among humans. Science, 328, 232-235
7. Luo K., and Hartemink A.J. (2013). using dnase digestion data to accuractely identify transcription factor binding sites. Pacific Symposium on Biocomputing, 80-91
8. Matsuda M., et al. (1992). d-thalassemia caused by disruption of the site for an erythroid-specific transcription factor, GATA-1, in the d-globin gene promoter. Blood, 80, 1347-1351
9. Neph S., et al. (2012). An expansive human regulatory lexicon encoded in transcription factor footprints. Nature, 489, 8390
10. Piper J., et al. (2013). Wellington: a novel method for the accurate identification of digital genomic footprints from dnase-seq data. Nucleic Acids Res., 41, e201
11. Pique-Regi R., et al. (2011). Accurate inference of transcription factor binding from dna sequence, and chromatin accessibility data. Genome Res., 21, 447-455
12. Ramsey S.A., et al. (2010). Genome-wide histone acetylation data improve prediction ofmammalian transcription factor binding sites. Bioinformatics, 26, 2071-2075
13. Sherwood R.I., et al. (2014). Discovery of directional, and nondirectional pioneer transcription factors by modeling dnase profile magnitude, and shape. Nat. Biotechnol., 32, 171-178
14. Sung M.-H., et al. (2014). Dnase footprint signatures are dictated by factor dynamics, and dna sequence. Mol. Cell, 56, 275-285
15. The ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74
16. Wang J., et al. (2012). Sequence features, and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res., 22, 1798-1812
17. Weirauch M.T., et al. (2013). Evaluation of methods for modeling transcription factor sequence specificity. Nat. Biotechnol., 31, 126-134
18. Wittwer J., et al. (2006). Functional polymorphism in ALOX15 results in increased allele-spesific transcription in macrophages through binding of the transcription factor SPI1. Hum. Mutat., 27, 78-87
19. Yardimci, et al. (2014). Explicit DNAse sequence bias modeling enables highresolution transcription factor footprint detection. Nucleic Acids Res., 42, 11865-11878