a ChIP-Seq case study - Genomatix

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Figure 5: ChIP-Seq workflow setup: All BED files uploaded within the active project are available for analysis and can be selected as treatment or control samples. For clustering, default settings (NGSAnalyzer with 100bp window size and automatic read density threshold calculation based on Poisson distribution) were used. Only clusters which were present in at least 2 replicates (65%) with an overlap of 100 bp were considered. For statistical evaluation of the remaining clusters edgeR was used (default). Further options, like ‘Cluster Classification and Statistics’, ‘Extraction of Sequences for all Clusters’, ‘Transcription Factor Binding Site Overrepresentation’, and ‘Definition of new Binding Sites in Clusters’ are selected by default. Figure 6: ChIP-Seq workflow setup: Selection of peak finding algorithm and parameter setup for replicate treatment and statistical analysis. As a last step, the analysis was named and submitted. © Genomatix 2012
Figure 7: Naming and submitting the analysis. After completion of the analysis, the result can be accessed through the link provided in the notification email or via the ‘Project Management’ under ‘Project & Accounts’ in the navigation bar. The result page lists the parameters and programs used and the results of the subtasks selected. All results can be downloaded or saved in the ‘Project Management’. The clustering results In this example, more than 10,000 clusters were called in the single samples, but only 8,291 are detected in at least two PPARgamma-day6-ChIP replicates. Of these 7,747 clusters show a statistical significant enrichment compared to the day0 controls. This number is comparable to the results from Nielsen et al. who report about 7,000 PPARgamma enriched regions. 11.6% of these are located in promoter regions, which corresponds to an 4.5 fold enrichment. All BED containing the positional information for the different cluster categories can be downloaded or saved in the „Project Management“ for further (more detailed) analyses. For this example it is sufficient to save the BED file for the significant enriched regions in the "Project Management" (PPARg_day6_vs_day0_enriched_regions.bed). Figure 8: ChIP-Seq workflow results: Clustering result overview shows that 8,291 PPARgamma peaks are found in at least 2 samples in day 6 but not in day 0. All detailed results can be downloaded. © Genomatix 2012
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Page 3: Downstream analysis Figure 3: Mappi
Page 7 and 8: The "Module overrepresentation" sub
Page 9 and 10: After submission, the regions will
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Page 13 and 14: Identification of common regulatory
Page 15 and 16: and V$EGRF with distances of roughl
Page 17 and 18: Figure 28: Visualization of the Scd

a ChIP-Seq case study - Genomatix

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