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.


TIGR [36]

Containing the information on the TSS and sequence location sites of Oryza genes from the annotations in TIGR.


ZmGDB [37]

Containing the information on the 2 kb upstream location sites of Zea genes from the annotations in ZmGDB.


Transcription factor binding sites

TRANSFAC public release 7.0 [11-13]

Collecting experimentally verified transcription factors, their genomic binding sites and DNA-binding profiles.


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.


AGRIS [17]

Collecting approximately 1,770 Arabidopsis transcription factors that are grouped into 50 families.


JASPER [18,19]

A popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns.


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.


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

Apriori [43,44]

Mining the co-occurrence of transcription factor binding sites in a group of gene promoters.


Chang et al. BMC Genomics 2008 9:561   doi:10.1186/1471-2164-9-561

Open Data