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

ABSTRACT:

Background

Sequence features in promoter regions are involved in regulating gene transcription initiation. Although numerous computational methods have been developed for predicting transcriptional start sites (TSSs) or transcription factor (TF) binding sites (TFBSs), they lack annotations for do not consider some important regulatory features such as CpG islands, tandem repeats, the TATA box, CCAAT box, GC box, over-represented oligonucleotides, DNA stability, and GC content. Additionally, the combinatorial interaction of TFs regulates the gene group that is associated with same expression pattern. To investigate gene transcriptional regulation, an integrated system that annotates regulatory features in a promoter sequence and detects co-regulation of TFs in a group of genes is ne

SUBMITTER: Lee TY 

PROVIDER: S-EPMC3587379 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature