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 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.