Data
To generate this track we used the Dnase-seq and histone modification
ChIP-seq data described in the corresponding tracks of this hub.
Methods
The identified DHS peaks were processed further to generate distinct
groups with different histone modification profiles. We divided first
the peaks into proximal or distal depending on whether they overlap the
promoter region (4000bp centred on the transcription start site (TSS))
defined for each transcript from Ensembl version 61.
Where multiple DHS peaks overlapped the same promoter, we only analysed
the DHS peak whose summit was closest to the TSS.
We used the K-means algorithm to define the different clusters of peaks,
as implemented in R (iter.max=100, nstart=3), according to the
normalized scores of the histone modification islands overlapping the
peaks.
We set the number of clusters by analysing the within groups sum of
squared error (SSE) so that a bigger number of clusters does not have a
substantial impact in the SSE (“elbow” method).
The resulting bed files were converted into bigBed files using the tool
bedToBigBed from the UCSC Genome Browser.
Credits
Data were generated and processed for the CISSTEM project. For inquiries, please contact Juan L. Mateo at the following address: mateojuan (at) uniovi.es
References
Mateo, J. L., van den Berg, D. L. C., Haeussler, M., Drechsel, D., Gaber, Z. B., Castro, D. S., ... Martynoga, B. (2015). Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome Research, 25(1), 41-56. DOI: 10.1101/gr.173435.114
|
|
US Server