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My input file of BED regions causes an error.

Ensure that your data is both valid BED format and either in plain text or using a supported compression format (currently .zip, .gz, .bz2, or .Z). If you download data from the UCSC Table Browser as BED format, be sure to leave the "Include custom track header" box unchecked, as that makes the file not a valid BED file.

The GREAT output page shows no enrichments for my input set.

The initial GREAT output display presents a "Summary View", which shows terms significant by both the binomial test over genomic regions and the hypergeometric test over genes. Summary view will show no or few enrichments if:

  1. Your set has no coherent functional signal. This is a biological phenomenon where GREAT identifies that your set has no shared signal. To see the most enriched terms, regardless of statistical significance, switch to "Full View" and lower or remove the "Binomial Fold Enrichment" filter.
  2. Your set is too small. If your input set consists of a very small number of regions (< 10), it is difficult to achieve statistical significance. While it is difficult for GREAT to identify shared signals in a small set, you can change to "Full View" to see the most enriched terms in your small set, regardless of whether the term enrichment achieves statistical significance.
  3. Your set is too large. Large data sets can cause a large fraction of all genes to be selected via the regulatory domain association rules. This often results in saturation of the hypergeometric test over genes such that no hypergeometric test results are significant. See Handling Large Datasets for tips on how best to run GREAT on large data sets.

The Term Details page contains a broken link for the ontology term.

We do not host all ontology information. Instead, we link to the source ontology (e.g. Gene Ontology) for a description of ontology terms. If the source changes the URL of an ontology term description, we will have a broken link until we correct our link to point to the new URL. We periodically examine all terms to correct broken links, but if you identify a broken link before we do, please notify us and we will correct it.

GREAT does not work well on my system.

See our list of supported browsers for operating system and web browser-specific issues.

A data set I analyzed previously now gives different results.

Make sure you are running the same GREAT version as you did previously.

The rank column is not showing consecutive numbers. What does this mean?

The rank column corresponds to the ordinal rank of the p-value compared to the p-value of other ontology terms. Output is sorted by region-based binomial p-value, so one might expect these numbers to be consecutive. However, GREAT has additional filters applied in its default display: displayed terms must also be significant by the gene-based hypergeometric test and must have a region-based fold enrichment of 2 or more. These filters may then cause some terms prioritized highly by the region-based binomial p-value alone to not be visualized.

Some links are not clickable.

Updates to GREAT sometimes change the way link clicks are handled. After a GREAT update, before using the site please clear your browser cache to ensure proper GREAT functionality.

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