Ensure that your data is both valid BED format and either in plain text or using a supported compression format (currently
.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 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:
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.
See our list of supported browsers for operating system and web browser-specific issues.
Make sure you are running the same GREAT version as you did previously.
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.
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.