a ChIP-Seq case study - Genomatix

Correlation between different data sets
PPARgamma binds to peroxisome proliferator response elements as a heterodimer with retinoic X receptor
(RXR) and RXR binding sites have been found to be overrepresented in the TF analysis (see above).
Therefore, it would be interesting to analyze the overlap between PPARgamma and RXR binding sites. The
RXR-ChIP data are derived from the same publication and have been processed similar to the PPARgamma
set.
Positional correlations between genomic elements and/or user data can be performed in the task
‘GenomeInspector’ which can be accessed from ‘NGS Analysis’ in the navigation bar. Using the
PPARgamma set as an anchor and calculating the distance distribution profile for the RXR data set results in
the curve shown in Figure 27. Regions contributing to the correlation can be extracted from both sets and
used for further analysis (e.g. annotation and pathway analysis or framework analysis).
Figure 27: Positional correlation of PPARgamma enriched regions (aligned with their middle at 0) with the RXR enriched regions
generated in GenomeInspector. The graph shows a clear overlap between the two data sets. Regions contributing to the correlation can
be extracted.
Data visualization
In the genome browser the data can be visualized in the genomic context, overlayed with general annotation,
proprietary data from Genomatix or other ChIP-Seq or RNA-Seq data sets. This allows an integration of
different datasets and a quick assessment of the state at the locus of interest. Figure 27 shows the Scd1
locus (located on the antisense strand) with PPARgamma, RXR and PolII raw reads and the positions of the
called clusters. The graph shows only background for the PPARgamma data at day 0 but a strong
enrichment at 5‘ promoter and several upstream and downstream regions, indicating potential enhancer
regions. The RXR data show a similar picture. At day 0, PolII is found at the potential enhancer regions and
the promoter. After adipocyte differentiation at day 6, PolII is no longer enriched at the promoter and
enhancers but spreads over the whole gene body - reflecting the PPARgamma expression.
© Genomatix 2012