The correlation information displayed in this tool has been pre-calculated by the epiGenomic Efficient Correlator (GeEC) tool (Laperle et al., https://doi.org/10.1093/bioinformatics/bty655) and imported in the IHEC Data Portal. The scores represent the Pearson product-moment correlation coefficients (r), using the average signal of each dataset calculated in bins of 1 kb over the whole genome, and excluding the ENCODE blacklisted regions (for hg19 and mm10). The displayed sub-matrix, composed of selected data from the Portal grid, is processed using the Python package scipy to generate the hierarchical clustering and the accompanying dendrogram.
The epiGeEC tool, wrapped in a public instance of Galaxy available here (epigeec.genap.ca), allows users to efficiently compare their own data with thousands of public datasets in a few minutes.
Dataset
Assay
Consortium
Message
Want a guided tour of the application?
Datasets grid
You can select or deselect datasets by clicking on the cells in the grid.
The currently selected datasets are shown in the Selected Datasets table
at the bottom of the page.
If you want to see those datasets in the USCS Genome Browser, click on
the Visualize in Genome Browser button.
At any point, you can save your current session by clicking on Save Session.
To get the IHEC Data Hub from the selected datasets, click Get Metadata.
It is also possible to add external data, either from one of our default source or
from your own IHEC Data Hub. For more informations, see the Add External Hub
button. Note that track correlation is not available with external data hubs.
If a dataset has an embargo, the institution datasets count will be displayed in red.
Click on that number to be brought to the relevant information page.
Search filtering
The search box accepts a list of expression formatted as: KEY = VALUE or KEY = "VALUE".
The operators = (equal to) and != (different than)
are available.
The expressions can be separated by either AND or OR.
Example search:
donor_age = 25 and donor_sex != "Male"
(Will find all datasets where the donor is 25 years old, and
is not a Male)
Visualization of correlation values on more than 300 datasets is currently not supported.
Alternatively, you can compute correlation scores on any number of datasets, including datasets external to IHEC, using the Genomic Efficient Correlator (GeEC) tool, offered within a public instance of Galaxy here.
Grid session link: Keep this URL to restore your current grid session.
UCSC track hub link: Can be used in any UCSC Browser setup, such as the main UCSC server.
First visit?
You can also watch it later in the "Click here for instructions"
link at the bottom right of the grid