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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.
As GREAT relies on a high-quality mappings of genes and their transcription start sites 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. This excludes loci where genes

References

Footnotes
Ref Notes
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
2

.

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 knownCanonical table of the UCSC Known Genes track<ref name="hsu">Hsu, F. et al. The UCSC Known Genes. Bioinformatics. 22(9):1036-1046 (2006).

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