期刊
NUCLEIC ACIDS RESEARCH
卷 34, 期 21, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkl803
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资金
- NIGMS NIH HHS [GM67250, R01 GM067250] Funding Source: Medline
Genome-wide location analysis (ChIP-chip, ChIP-PET) is a powerful technique to study mammalian transcriptional regulation. In order to obtain a basic understanding of the location data generated for mammalian transcription factors and potential issues in their analysis, we conducted a comparative study of eight independent ChIP experiments involving six different transcription factors in human and mouse. Our cross-study comparisons, to the best of our knowledge the first to analyze multiple datasets, revealed the importance of carefully chosen genomic controls in the de novo identification of key transcription factor binding motifs, raised issues about the interpretation of ubiquitously occurring sequence motifs, and demonstrated the clustering tendency of protein-binding regions for certain transcription factors.
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