Los servicios en los esquemas de integración: algunas consideraciones y opciones para Centroamérica: versión provisional

Incluye Bibliografí

Number of Peaks Detected by Each Peak Caller Using Their Default Parameters.

<p>The number of peaks obtained by each algorithm at their default signal threshold.</p

F Scores of Algorithms Over Three Cell Types from the “Double Hit” Protocol.

<p>Each algorithm was evaluated to gauge the enrichment of short read tags in each of the three cell types obtained from University of Washington “double hit” protocol <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096303#pone.0096303-Sabo1" target="_blank">[27]</a>. The overlap of peaks from each of the cell types was measured against the cell type's “reference set of regulatory regions”. The accuracy of each algorithm was defined as the value of the F score (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096303#s4" target="_blank">Methods</a> for more details) by running it over a range of thresholds. The dashed vertical grey line depicts the value of F score when the algorithm is run with its default parameter. Note that Hotspot failed when ran with  = 0.3 for HelaS3 cell type and therefore its corresponding curve is shorter by one data point.</p

Comparison of the Peak Calling Algorithms Based on Estimated True Positive and False Discovery Rates.

<p>Each algorithm was run over 13 values of a parameter that controls the false discovery. These values for Hotspot, MACS and ZINBA range from 0.001 to 0.2 and for F-Seq it ranges from 0.001 up to 6 (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096303#s4" target="_blank">methods</a> for more details). For each value the overlap between the calls and the “reference set of regulatory regions” for that cell type was measured. The black dots show the default value for each algorithm.</p

Coverage of Peaks Detected by Each Peak Caller Using Their Default Parameters.

<p>Illustrated here is the percentage of chromosome 22 covered by peaks from each peak caller over three cell type.</p

DNase I Peak Callers Benchmarked in This Study.

<p>This table shows a number of properties of the four peak calling algorithms used in this study, highlighting some of the differences (as evaluated on a Intel(R) Xeon(R) CPU @ machine). The CPU Time in seconds was obtained when running each algorithm on the K562 data (for the other two cell type comparable figures are obtained, data not shown). The Max Memory column shows the maximum memory used by the algorithm. The numbers in parentheses show the maximum number of processes used when generating this data. For MACS and ZINBA control data is optional and is believed to improve the accuracy of the algorithm, but in this study all algorithms have been run without control data sets. Hotspot and ZINBA require mappability data and both algorithms provide it for a set of specific lengths including 36 bp. The core Hotspot algorithm is implemented in , however the Hotspot pipeline involves <i>R</i>, python and bash scripts. ZINBA comes as an <i>R</i> package having its core implemented in <i>C</i>.</p

Additional file 4: of Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity

A tab-formatted text file containing the results of the PCHi-C randomization preserving network topology. (TXT 157 kb

Replication timing of repetitive elements in wild-type and mutant ES cell lines

The replication timing was determined for retrotransposons (LINE and SINE B1) and rDNA repeats in wild-type OS25 ES cells and in mutant ES cells lacking Eed, Dnmt 1, Dnmt 3a/3b, G9a or Dicer. The mean values and standard error of at least two independent experiments are shown.<p><b>Copyright information:</b></p><p>Taken from "The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells"</p><p>http://genomebiology.com/2007/8/8/R169</p><p>Genome Biology 2007;8(8):R169-R169.</p><p>Published online 17 Aug 2007</p><p>PMCID:PMC2374999.</p><p></p

Satellite replication in ES cells is altered by mutation of chromatin modifiers

Summary of replication timing of repeat sequences in mutant ES cell lines. Top, ideogram of the acrocentric mouse chromosome X, showing the position of minor satellite (Minor sat), major satellite (Major sat) and the X-linked X141 repeat. Examples show replication timing of repeats in wild type (WT, white bars (OS25 for Mll, Eed and Dnmt1; matched wild-type lines for G9a, Suv39 h1/h2 and Dicer)) compared to ES cells mutant for the indicated chromatin modifier (black bars). The mean values and standard error of at least two (two to five) independent experiments are shown.<p><b>Copyright information:</b></p><p>Taken from "The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells"</p><p>http://genomebiology.com/2007/8/8/R169</p><p>Genome Biology 2007;8(8):R169-R169.</p><p>Published online 17 Aug 2007</p><p>PMCID:PMC2374999.</p><p></p

Additional file 3: of CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data

The CHiCAGO R package tutorial. (PDF 946 kb