Which set of genes does GREAT use?
To limit the gene sets to only extremely high-confidence gene predictions, GREAT uses only the subset of the UCSC Known Genes<ref name="hsu">Hsu, F. et al. The UCSC Known Genes. Bioinformatics. 22(9):1036-1046 (2006).1 Ashburner M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium, Nat Genet. 25(1):25-29 (2000).2 .
Zebrafish gene set
The zebrafish genome has no gold-standard set of coding genes that are mapped to the danRer6 and danRer7 genomes. Furthermore, most ontology data is linked to ZFIN gene identifiers, however, ZFIN genes are not mapped to the genome.
As GREAT relies on a high-quality mappings of genes to the genome, we used the following transcript/gene sources to create the gene set:
- RefSeq transcripts
- Ensembl coding genes
- RefSeq proteins
- Uniprot proteins
We mapped these transcripts and proteins using Blat requiring that at least 80% of the sequence matches with at least 95% identity to one co-linear locus in the zebrafish genome. These filters are stringent enough to avoid gene loci where only a fraction of the gene matches. This step is crucial, as inflating the number of loci for a gene compromises GREAT's statistical tests. Furt
We retained only the best hit per locus, which effectively handles matches of paralogs. As a substantial number of bona-fide genes map to scaffolds, we include all gene-containing scaffolds in zebrafish GREAT.
Our set of reliably mapped genes contains 14,039 genes mapped to 14,834 genomic loci for danRer6.
From the 16,434 RefSeq transcripts that are associated to a ZFIN gene ID, our gene set contains 13,002 (79%).
From the 13104 Ensembl genes that are associated to a ZFIN gene ID, our gene set contains 12,378 (94.5%).
|1||that are protein-coding (cdsStart != cdsEnd), are on non-random and non-haplotype chromosomes, and possess at least one meaningful Gene Ontology (GO) annotation|
GO includes information on the biological processes, cellular components, and molecular functions of genes. Thus, GREAT assumes that if a gene has been annotated for function at all then it is annotated in GO. Uninformative GO terms that do not allow entry into the gene set are 'Gene Ontology', 'biological process', 'cellular component', 'molecular function', 'obsolete biological process', 'obsolete cellular component', and 'obsolete molecular function'.
How does GREAT determine a single transcription start site for each gene?
Many genes have multiple splice variants, however the vast majority of annotations available for these genes do not (and often cannot) distinguish between the different isoforms. Motivated by this observation, GREAT uses a single transcription start site to represent each gene in calculating gene regulatory domains. So, GREAT uses the transcription start site of the canonical isoform of a gene. The definition of the canonical isoform is taken from the