PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
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Home TFext BLAST Prediction Download Help About Links PlantRegMap |
- The flowchart for construction of PlantTFDB
- Data source
- Data source (TFext)
- Pipeline to construct comprehensive protein dataset
- Family assignment rules
- List of studies which use the Family assignment rules
- Thresholds for domain identification
- Summary of TFs in different taxonomic lineages of green plants and the origination stage of TF families
- Pipeline for parsing BLAST reciprocal best hits (RBHs) and inferring orthologous groups
- Pipeline for GO annotation
- Curation and projection of TF binding motifs
- Transcription factor information
- Multiple sequence alignment
- Phylogenetic trees
- Quick search
- TF prediction server
- Help for PlantRegMap
Pipeline for GO annotation
GO terms were assigned to the genes of 165 species as follows:
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.
- 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.
- 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)'.
- '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)'.
- 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.