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Table 1 Supported regulatory features in GPMiner

From: GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group

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