Table 1

Supported regulatory features in GPMiner

Regulatory features

Integrated database or tools

Descriptions


Transcriptional start site

NNPP2.2 [14]

Applying a time-delay neural network for promoter annotation


McPromoter [16]

Using a statistical method to identify eukaryotic polymerase II TSS in genomic DNA


Eponine [15]

Predicting the transcription start site for a DNA sequence with prediction specificity > 70%


Transcription factor (TF) binding site

TRANSFAC public release 7.0 [46]

Storing the experimentally verified transcription factors, their genomic binding sites and DNA-binding profiles


MATCH [29]

Scanning the transcription factor binding site using the transcription factor binding profiles from TRANSFAC public release 7.0 and JASPAR


CpG island

CpGProD [12]

Detecting the CpG island


Repeats

TRF [32]

A tandem repeat finder


TATA box, CCAAT box, and GC box

MATCH [29]

Scanning the TATA-, CCAAT- and GC-box by the transcription factor binding profiles from TRANSFAC


Narang et al. [47]

Defining the 6-mer pattern of the TATA box, CCAAT box, and GX box with positional density


Over-represented pattern

Huang et al. [48]

Defining the statistically significant pattern in the promoter region


DNA stability

Aditi Kanhere et al. [21]

Predicting the DNA stability of the promoter region


Co-occurrence of TF binding sites

apriori [35]

A method to mine the association rules


Conserved regions between homologous gene promoter sequences

Blast [25]

Using the blast program to analyze the conserved region between the homologous gene promoter sequences


Lee et al. BMC Genomics 2012 13(Suppl 1):S3   doi:10.1186/1471-2164-13-S1-S3

Open Data