Plant Transcription Factor Database
Previous version: v1.0, v2.0, v3.0
Pipeline for GO annotation
GO terms were assigned to the genes of 165 species as follows:
  1. GO annotation was collected from TAIR10 and UniProtKB, with 'NOT' qualifier and that from InterPro filtered out. The resulted GO annotation was divided into two sets: that with experimental evidence codes (i.e., IDA, IPI, IMP, IGI and IEP; labeled as 'TU_E') and that without (labeled as 'TU_NE'). The redundant annotation with parental/ancient terms in 'TU_E' and 'TU_NE' was filtered out, respectively, if more specific child terms existed.
  2. The GO annotation for all genes from 165 species was predicted by InterProScan 5 according to the GO annotation guidance 'GO_REF:0000002'. This annotation received the evidence code 'IEA' with the source labeled as 'PlantRegMap(InterPro)'.
  3. 'TU_E' annotation of genes was projected to their RBHs in other species by referring the GO annotation guidance 'GO_REF:0000035'. The annotation with GO:0005515 (protein binding) was not projected. This annotation received the evidence code 'IEA' with the source labeled as 'PlantRegMap(RBH)'.
  4. GO annotation from TU_NE, PlantRegMap(InterPro) and PlantRegMap(RBH) was merged, and redundant annotation was filtered out using 'TU_E' and then itself, respectively. The resulted GO annotation was merged with 'TU_E'.

The GO annotation of TFs can be viewed at the information page of corresponding TFs, and the GO annotation of all can be accessed at the download page of the new portal PlantRegMap. Users can perform GO enrichment analysis here for 165 species based on this data.