Gene Family Annotation Method

Our gene family annotation method follows the standards set by AnimalTFDB (Animal Transcription Factor Database) version 4.0, in combination with the latest Ensembl data. Our approach ensures accuracy and consistency in gene family classification and threshold setting. Specifically, our method is based on AnimalTFDB4.0, with adjustments made to the thresholds of certain families to better suit our data.

To adapt to the latest versions of Ensembl fasta and gtf files, we adjusted the thresholds for several transcription factor (TF) families. For example, the threshold for the Fork_head and MYB families has been set to 1e-2, while the threshold for the Homeobox family was adjusted to 1e-3. These adjustments help improve the accuracy of annotations, especially when the boundaries between gene families are unclear.

More information about the gene family annotation method can be found in the AnimalTFDB4.0 documentation.