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ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data

Creators: Buck, Michael J, Nobel, Andrew B, Lieb, Jason D

  • File Type: pdf | Filesize: 319.5 KB
  • Date Deposited: 2012-09-05
  • Date Created: 2005-10-19

Abstract ChIPOTle (Chromatin ImmunoPrecipitation On Tiled arrays) takes advantage of two unique properties of ChIP-chip data: the single-tailed nature of the data, caused by specific enrichment but not specific depletion of genomic fragments; and the predictable enrichment of DNA fragments adjacent to sites of direct protein-DNA interaction. Implemented as a Microsoft Excel macro written in Visual Basic, ChIPOTle uses a sliding window approach that yields improvements in the identification of bona fide sites of protein-DNA interaction.