Identification and Functional Annotation of Genome-Wide ER-Regulated Genes in Breast Cancer Based on ChIP-Seq Data

<div class="floats-full-page floats-full-page-other"><h2>Table 2</h2><div class="floats-full-page-caption">An overview of the characteristics of different Chip-Seq peak detection algorithm.</div><div class="floats-full-page-content"><table class="table-group" id="tab2"><tr><td><table class="table"><tr><td class="thead-hr" colspan="5"><hr /></td></tr><tr><td align="left">Algorithm</td><td align="center">Profile</td><td align="center">Background model</td><td align="center">Control sample</td><td align="center">Use control to compute FDR</td></tr><tr><td align="left" colspan="5"><hr /></td></tr><tr><td align="left">F-Seq</td><td align="center">Kernel density estimation (KDE)</td><td align="center"> </td><td align="center"><span style="width: 13.1125px;"><svg height="17.125" id="M1" style="vertical-align:-5.4327pt" version="1.1" viewbox="0 0 13.1125 17.125" width="13.1125" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,12.862)"><path d="M782 703l-309 -950l-231 505l-91 -47l-18 35l147 78l194 -431h2l264 810h42z" id="x221A"></path></g>
</svg></span></td><td align="center"> </td></tr><tr><td align="left">FindPeaks</td><td align="center">Aggregation of overlapped tags</td><td align="center">Monte Carlo</td><td align="center"> </td><td align="center"> </td></tr><tr><td align="left">SISSRs</td><td align="center">Window scan</td><td align="center">Poisson</td><td align="center"><span style="width: 13.1125px;"><svg height="17.125" id="M2" style="vertical-align:-5.4327pt" version="1.1" viewbox="0 0 13.1125 17.125" width="13.1125" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,12.862)"><path d="M782 703l-309 -950l-231 505l-91 -47l-18 35l147 78l194 -431h2l264 810h42z" id="x221A"></path></g>
</svg></span></td><td align="center"> </td></tr><tr><td align="left">QuEST</td><td align="center">Kernel density estimation (KDE)</td><td align="center"> </td><td align="center"><span style="width: 13.1125px;"><svg height="17.125" id="M3" style="vertical-align:-5.4327pt" version="1.1" viewbox="0 0 13.1125 17.125" width="13.1125" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,12.862)"><path d="M782 703l-309 -950l-231 505l-91 -47l-18 35l147 78l194 -431h2l264 810h42z" id="x221A"></path></g>
</svg></span></td><td align="center"><span style="width: 13.1125px;"><svg height="17.125" id="M4" style="vertical-align:-5.4327pt" version="1.1" viewbox="0 0 13.1125 17.125" width="13.1125" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,12.862)"><path d="M782 703l-309 -950l-231 505l-91 -47l-18 35l147 78l194 -431h2l264 810h42z" id="x221A"></path></g>
</svg></span></td></tr><tr><td align="left">MACS</td><td align="center">Tags shifted then window scan</td><td align="center">dynamic Poisson</td><td align="center"><span style="width: 13.1125px;"><svg height="17.125" id="M5" style="vertical-align:-5.4327pt" version="1.1" viewbox="0 0 13.1125 17.125" width="13.1125" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,12.862)"><path d="M782 703l-309 -950l-231 505l-91 -47l-18 35l147 78l194 -431h2l264 810h42z" id="x221A"></path></g>
</svg></span></td><td align="center"><span style="width: 13.1125px;"><svg height="17.125" id="M6" style="vertical-align:-5.4327pt" version="1.1" viewbox="0 0 13.1125 17.125" width="13.1125" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,12.862)"><path d="M782 703l-309 -950l-231 505l-91 -47l-18 35l147 78l194 -431h2l264 810h42z" id="x221A"></path></g>
</svg></span></td></tr><tr><td align="left">CisGenome</td><td align="center">Strand-specific window scan</td><td align="center">Negative binomial</td><td align="center"><span style="width: 13.1125px;"><svg height="17.125" id="M7" style="vertical-align:-5.4327pt" version="1.1" viewbox="0 0 13.1125 17.125" width="13.1125" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,12.862)"><path d="M782 703l-309 -950l-231 505l-91 -47l-18 35l147 78l194 -431h2l264 810h42z" id="x221A"></path></g>
</svg></span></td><td align="center"><span style="width: 13.1125px;"><svg height="17.125" id="M8" style="vertical-align:-5.4327pt" version="1.1" viewbox="0 0 13.1125 17.125" width="13.1125" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g transform="matrix(.017,-0,0,-.017,.062,12.862)"><path d="M782 703l-309 -950l-231 505l-91 -47l-18 35l147 78l194 -431h2l264 810h42z" id="x221A"></path></g>
</svg></span></td></tr><tr class="table-tr"><td colspan="5"><hr class="tbody-hr" /></td></tr></table></td></tr></table></div></div>

Table 2 | Identification and Functional Annotation of Genome-Wide ER-Regulated Genes in Breast Cancer Based on ChIP-Seq Data

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Table 2: Identification and Functional Annotation of Genome-Wide ER-Regulated Genes in Breast Cancer Based on ChIP-Seq Data

description

Table 2

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