Table 2 Supported regulatory features in PlantPAN.
Transcriptional Regulatory Features | Integrated Databases or Tools | Descriptions |
|---|---|---|
Promoter sequences and location sites | TAIR [35] | Containing the information on the TSS and sequence location sites of Arabidopsis genes from the annotations in TAIR. |
| Â | TIGR [36] | Containing the information on the TSS and sequence location sites of Oryza genes from the annotations in TIGR. |
| Â | ZmGDB [37] | Containing the information on the 2 kb upstream location sites of Zea genes from the annotations in ZmGDB. |
Transcription factor binding sites | Collecting experimentally verified transcription factors, their genomic binding sites and DNA-binding profiles. | |
| Â | PLACE [16] | A database of nucleotide sequence motifs found in plant cis-acting regulatory DNA elements. Motifs were extracted from previously published reports on genes in vascular plants. |
| Â | AGRIS [17] | Collecting approximately 1,770 Arabidopsis transcription factors that are grouped into 50 families. |
| Â | A popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. | |
| Â | MATCH [40] | Scanning transcription factor binding sites using transcription factor binding profiles from TRANSFAC and PLACE. |
CpG/CpNpG islands | CpGProD [29] | Detecting CpG/CpNpG islands. |
Tandem repeats | TRF [34] | Finding the tandem repeat. |
Conservation of homologous gene promoter sequences | BLAST [46] | Searching sequence similarity; it is also used for discovering similar gene promoters and identifying conserved regions in the PlantPAN assistant promoter database. |
| Â | BL2SEQ [47] | Utilizing the BLAST algorithm for identifying conserved regions in two sequences. |
Co-occurrence transcription factor binding sites in a gene group of gene promoters | Mining the co-occurrence of transcription factor binding sites in a group of gene promoters. |