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<h1><a href="http://piq.csail.mit.edu"><font color="#000000">PIQ: Protein Interaction Quantification</font></a></h1>


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<td class="toplinks"><a href="index.html">PIQ Overview</a></td>
<td class="toplinks"><a href="algorithm.html">Algorithm Design</a></td>
<td class="toplinks"><a href="results.html">Binding calls</a></td>
<td class="toplinks"><a href="download.html">Code</a></td>
<td class="toplinks"><a href="contact.html">Contact</a></td>
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<tr><td colspan=6 class="refbody">

PIQ is a new computational method that uses machine learning to identify the
genomic binding sites of hundreds of transcription factors (TFs) at
corresponding motifs from DNase-Seq experiments with accuracy comparable to ChIP-Seq.
We employed PIQ in a developmental lineage paradigm of pancreatic endoderm
specification from embryonic stem cells and identified a set of novel pioneer TFs
that dynamically open chromatin in the lineage and enable other TFs to bind to adjacent DNA.
Surprisingly, several pioneer TFs with non-palindromic motifs only open chromatin
in one direction. We found that genomic binding of a distinct subset of settler TFs
depends on proximity to chromatin opened by pioneer TFs.  In vivo experiments
confirmed directional and non-directional pioneer activity and settler binding.

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