A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä
A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
Tekijät: Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo LL
Kustantaja: BIOMED CENTRAL LTD
Julkaisuvuosi: 2009
Journal: BMC Genomics
Tietokannassa oleva lehden nimi: BMC GENOMICS
Lehden akronyymi: BMC GENOMICS
Artikkelin numero: ARTN 618
Vuosikerta: 10
Sivujen määrä: 15
ISSN: 1471-2164
DOI: https://doi.org/10.1186/1471-2164-10-618
Verkko-osoite: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2804666/pdf/1471-2164-10-618.pdf
Background: Chromatin immunoprecipitation coupled with massively parallel sequencing (ChIPseq)
is increasingly being applied to study transcriptional regulation on a genome-wide scale. While
numerous algorithms have recently been proposed for analysing the large ChIP-seq datasets, their
relative merits and potential limitations remain unclear in practical applications.
Results: The present study compares the state-of-the-art algorithms for detecting transcription
factor binding sites in four diverse ChIP-seq datasets under a variety of practical research settings.
First, we demonstrate how the biological conclusions may change dramatically when the different
algorithms are applied. The reproducibility across biological replicates is then investigated as an
internal validation of the detections. Finally, the predicted binding sites with each method are
compared to high-scoring binding motifs as well as binding regions confirmed in independent qPCR
experiments.
Conclusions: In general, our results indicate that the optimal choice of the computational
approach depends heavily on the dataset under analysis. In addition to revealing valuable
information to the users of this technology about the characteristics of the binding site detection
approaches, the systematic evaluation framework provides also a useful reference to the
developers of improved algorithms for ChIP-seq data.
Ladattava julkaisu This is an electronic reprint of the original article. |  |
