IC4R003-Epigenomic-2011-21984925 - Revision history

Xysj1990: /* Research Findings */

2016-06-22T07:47:13Z

‎Research Findings

Xysj1990: /* Research Findings */

2016-06-22T07:46:53Z

‎Research Findings

Xysj1990: /* Research Findings */

2016-06-22T07:46:32Z

‎Research Findings

Xysj1990: /* Research Findings */

2016-06-22T07:45:50Z

‎Research Findings

Xysj1990: /* Research Findings */

2016-06-22T07:45:35Z

‎Research Findings

Xysj1990: /* Research Findings */

2016-06-22T07:43:17Z

‎Research Findings

Xysj1990: /* Research Findings */

2016-06-22T07:42:02Z

‎Research Findings

Xysj1990: /* Research Findings */

2016-06-22T07:41:16Z

‎Research Findings

Xysj1990: /* Plant Materials & Treatment */

2016-06-22T07:41:03Z

‎Plant Materials & Treatment

Xysj1990: /* Plant Materials & Treatment */

2016-06-22T04:49:35Z

‎Plant Materials & Treatment

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 * The results show that the average peak bandwidth called by PeakSeq ranges from 2,393 bp to 11,284 bp depending on the max_gap parameter. Smaller values of the max_gap parameter result in shorter peak bandwidths. In the remainder of this manuscript, all PeakSeq results use max_gap = 200 and the program is referred to as PeakSeq(200). The peaks produced by FindPeaks have an average bandwidth of 846 bp while those identified by Useq average 2,313 bp—similar to those identified by PeakSeq(200). The peak bandwidth identified by MACS is the shortest at 778 bp on average.<br><br>
-[[File:IC4R003-Epigenomic-2011-21984925-2.png |center |thumb |1000px|'''Figure 1. GBrowse visualization of identified peaks.''']]<br><br>
+[[File:IC4R003-Epigenomic-2011-21984925-2.png |center |thumb |1000px|'''Figure 1. GBrowse visualization of identified peaks.''']]<br>
 * FindPeaks identified 41,516 peaks covering 9.0% of the genome, USeq identified 9,094 peaks covering 5.4% of the genome, and MACS identified 15,738 peaks covering 3.1% of the genome. In contrast, peaks identified by PeakSeq with different max_gap values covers from 44% to 68.9% of the genome and identifies from 23,760 to 71,269 peaks.
 * Figure 2 displays the distribution of peaks identified by each of the peak identification programs. It is clear that the peaks identified by different programs displayed substantial differences. MACS, USeq, FindPeaks and PeakSeq(200) identified 97%, 86%, 65% and 20% of the total genes with no peak, respectively. For H3K27me3 peaks identified to be within a gene, the ratio was 2% for MACS, 5% for USeq, 22% for FindPeaks, and 71% for PeakSeq. For H3K27me3 peaks in the promoter region, the ratio was about 0.6% for MACS, 5% for USeq, 7% for FindPeaks, and 5% for PeakSeq. For the H3K27me3 peaks downstream of a gene, the ratio was about 0.4% for MACS, 4% for USeq, 6% for FindPeaks and 4% for PeakSeq, respectively. These results demonstrate that different programs will identify different peaks although the same dataset is used.

@@ Line 14: / Line 14: @@
 * The results show that the average peak bandwidth called by PeakSeq ranges from 2,393 bp to 11,284 bp depending on the max_gap parameter. Smaller values of the max_gap parameter result in shorter peak bandwidths. In the remainder of this manuscript, all PeakSeq results use max_gap = 200 and the program is referred to as PeakSeq(200). The peaks produced by FindPeaks have an average bandwidth of 846 bp while those identified by Useq average 2,313 bp—similar to those identified by PeakSeq(200). The peak bandwidth identified by MACS is the shortest at 778 bp on average.<br><br>
-[[File:IC4R003-Epigenomic-2011-21984925-2.png |center |thumb |1000px|'''Figure 1. GBrowse visualization of identified peaks.''']]
+[[File:IC4R003-Epigenomic-2011-21984925-2.png |center |thumb |1000px|'''Figure 1. GBrowse visualization of identified peaks.''']]<br><br>
 * FindPeaks identified 41,516 peaks covering 9.0% of the genome, USeq identified 9,094 peaks covering 5.4% of the genome, and MACS identified 15,738 peaks covering 3.1% of the genome. In contrast, peaks identified by PeakSeq with different max_gap values covers from 44% to 68.9% of the genome and identifies from 23,760 to 71,269 peaks.
 * Figure 2 displays the distribution of peaks identified by each of the peak identification programs. It is clear that the peaks identified by different programs displayed substantial differences. MACS, USeq, FindPeaks and PeakSeq(200) identified 97%, 86%, 65% and 20% of the total genes with no peak, respectively. For H3K27me3 peaks identified to be within a gene, the ratio was 2% for MACS, 5% for USeq, 22% for FindPeaks, and 71% for PeakSeq. For H3K27me3 peaks in the promoter region, the ratio was about 0.6% for MACS, 5% for USeq, 7% for FindPeaks, and 5% for PeakSeq. For the H3K27me3 peaks downstream of a gene, the ratio was about 0.4% for MACS, 4% for USeq, 6% for FindPeaks and 4% for PeakSeq, respectively. These results demonstrate that different programs will identify different peaks although the same dataset is used.

@@ Line 9: / Line 9: @@
 ==Research Findings==
-* Four peak calling programs (MACS [10], PeakSeq [8], FindPeaks version 3.1.9 [4], and USeq [7]) were used to identify peaks of the mapped reads, respectively. '''Table 1''' summarizes characteristics of the peaks identified by each of the programs and '''Figure 1''' shows an example of some of the peaks identified by the different programs displayed in GBrowse [30]. This image displays a 200 kb region of rice chromosome 1. The top track indicates the positions of all genes identified by TIGR, v6. The next two tracks display the distribution of ChIP and Input (control) reads respectively. The following four tracks display the predicted peaks by each of the four examined peak calling programs. The sequence read numbers were normalized to ensure that the ChIP and the Input had identical read numbers over the total genome. Therefore, the height of the graph in this figure directly correlates with the read number in the region to visually display the DNA enrichment.
+* Four peak calling programs (MACS [10], PeakSeq [8], FindPeaks version 3.1.9 [4], and USeq [7]) were used to identify peaks of the mapped reads, respectively. '''Table 1''' summarizes characteristics of the peaks identified by each of the programs and '''Figure 1''' shows an example of some of the peaks identified by the different programs displayed in GBrowse [30]. This image displays a 200 kb region of rice chromosome 1. The top track indicates the positions of all genes identified by TIGR, v6. The next two tracks display the distribution of ChIP and Input (control) reads respectively. The following four tracks display the predicted peaks by each of the four examined peak calling programs. The sequence read numbers were normalized to ensure that the ChIP and the Input had identical read numbers over the total genome. Therefore, the height of the graph in this figure directly correlates with the read number in the region to visually display the DNA enrichment.<br><br>
 [[File:IC4R003-Epigenomic-2011-21984925-1.png |center |thumb |1000px|]]
-* The results show that the average peak bandwidth called by PeakSeq ranges from 2,393 bp to 11,284 bp depending on the max_gap parameter. Smaller values of the max_gap parameter result in shorter peak bandwidths. In the remainder of this manuscript, all PeakSeq results use max_gap = 200 and the program is referred to as PeakSeq(200). The peaks produced by FindPeaks have an average bandwidth of 846 bp while those identified by Useq average 2,313 bp—similar to those identified by PeakSeq(200). The peak bandwidth identified by MACS is the shortest at 778 bp on average.
+* The results show that the average peak bandwidth called by PeakSeq ranges from 2,393 bp to 11,284 bp depending on the max_gap parameter. Smaller values of the max_gap parameter result in shorter peak bandwidths. In the remainder of this manuscript, all PeakSeq results use max_gap = 200 and the program is referred to as PeakSeq(200). The peaks produced by FindPeaks have an average bandwidth of 846 bp while those identified by Useq average 2,313 bp—similar to those identified by PeakSeq(200). The peak bandwidth identified by MACS is the shortest at 778 bp on average.<br><br>
 [[File:IC4R003-Epigenomic-2011-21984925-2.png |center |thumb |1000px|'''Figure 1. GBrowse visualization of identified peaks.''']]
 * FindPeaks identified 41,516 peaks covering 9.0% of the genome, USeq identified 9,094 peaks covering 5.4% of the genome, and MACS identified 15,738 peaks covering 3.1% of the genome. In contrast, peaks identified by PeakSeq with different max_gap values covers from 44% to 68.9% of the genome and identifies from 23,760 to 71,269 peaks.

@@ Line 14: / Line 14: @@
 * The results show that the average peak bandwidth called by PeakSeq ranges from 2,393 bp to 11,284 bp depending on the max_gap parameter. Smaller values of the max_gap parameter result in shorter peak bandwidths. In the remainder of this manuscript, all PeakSeq results use max_gap = 200 and the program is referred to as PeakSeq(200). The peaks produced by FindPeaks have an average bandwidth of 846 bp while those identified by Useq average 2,313 bp—similar to those identified by PeakSeq(200). The peak bandwidth identified by MACS is the shortest at 778 bp on average.
-[[File:IC4R003-Epigenomic-2011-21984925-3.png |center |thumb |1000px|'''Figure 1. GBrowse visualization of identified peaks.''']]
+[[File:IC4R003-Epigenomic-2011-21984925-2.png |center |thumb |1000px|'''Figure 1. GBrowse visualization of identified peaks.''']]
 * FindPeaks identified 41,516 peaks covering 9.0% of the genome, USeq identified 9,094 peaks covering 5.4% of the genome, and MACS identified 15,738 peaks covering 3.1% of the genome. In contrast, peaks identified by PeakSeq with different max_gap values covers from 44% to 68.9% of the genome and identifies from 23,760 to 71,269 peaks.
 * Figure 2 displays the distribution of peaks identified by each of the peak identification programs. It is clear that the peaks identified by different programs displayed substantial differences. MACS, USeq, FindPeaks and PeakSeq(200) identified 97%, 86%, 65% and 20% of the total genes with no peak, respectively. For H3K27me3 peaks identified to be within a gene, the ratio was 2% for MACS, 5% for USeq, 22% for FindPeaks, and 71% for PeakSeq. For H3K27me3 peaks in the promoter region, the ratio was about 0.6% for MACS, 5% for USeq, 7% for FindPeaks, and 5% for PeakSeq. For the H3K27me3 peaks downstream of a gene, the ratio was about 0.4% for MACS, 4% for USeq, 6% for FindPeaks and 4% for PeakSeq, respectively. These results demonstrate that different programs will identify different peaks although the same dataset is used.

@@ Line 10: / Line 10: @@
 ==Research Findings==
 * Four peak calling programs (MACS [10], PeakSeq [8], FindPeaks version 3.1.9 [4], and USeq [7]) were used to identify peaks of the mapped reads, respectively. '''Table 1''' summarizes characteristics of the peaks identified by each of the programs and '''Figure 1''' shows an example of some of the peaks identified by the different programs displayed in GBrowse [30]. This image displays a 200 kb region of rice chromosome 1. The top track indicates the positions of all genes identified by TIGR, v6. The next two tracks display the distribution of ChIP and Input (control) reads respectively. The following four tracks display the predicted peaks by each of the four examined peak calling programs. The sequence read numbers were normalized to ensure that the ChIP and the Input had identical read numbers over the total genome. Therefore, the height of the graph in this figure directly correlates with the read number in the region to visually display the DNA enrichment.
 * The results show that the average peak bandwidth called by PeakSeq ranges from 2,393 bp to 11,284 bp depending on the max_gap parameter. Smaller values of the max_gap parameter result in shorter peak bandwidths. In the remainder of this manuscript, all PeakSeq results use max_gap = 200 and the program is referred to as PeakSeq(200). The peaks produced by FindPeaks have an average bandwidth of 846 bp while those identified by Useq average 2,313 bp—similar to those identified by PeakSeq(200). The peak bandwidth identified by MACS is the shortest at 778 bp on average.
 * FindPeaks identified 41,516 peaks covering 9.0% of the genome, USeq identified 9,094 peaks covering 5.4% of the genome, and MACS identified 15,738 peaks covering 3.1% of the genome. In contrast, peaks identified by PeakSeq with different max_gap values covers from 44% to 68.9% of the genome and identifies from 23,760 to 71,269 peaks.
 * Figure 2 displays the distribution of peaks identified by each of the peak identification programs. It is clear that the peaks identified by different programs displayed substantial differences. MACS, USeq, FindPeaks and PeakSeq(200) identified 97%, 86%, 65% and 20% of the total genes with no peak, respectively. For H3K27me3 peaks identified to be within a gene, the ratio was 2% for MACS, 5% for USeq, 22% for FindPeaks, and 71% for PeakSeq. For H3K27me3 peaks in the promoter region, the ratio was about 0.6% for MACS, 5% for USeq, 7% for FindPeaks, and 5% for PeakSeq. For the H3K27me3 peaks downstream of a gene, the ratio was about 0.4% for MACS, 4% for USeq, 6% for FindPeaks and 4% for PeakSeq, respectively. These results demonstrate that different programs will identify different peaks although the same dataset is used.

@@ Line 7: / Line 7: @@
 ==Plant Materials & Treatment==
 * All plants used in this study were rice strain Oryza sativa ssp japonica cv Nipponbare. The immature rice seeds were harvested 6–7 days after pollination. The cross-linking of the chromatin was achieved by vacuum infiltrating PBS (pH7.4) with 1% formaldehyde for 15 min at room temperature. The cross-linking reaction was stopped by adding glycine to a final concentration of 0.125 M and incubating for 5 min under vacuum. The tissues were rinsed 3 times with PBS.
 ==Labs working on this Project==