Distinct epigenetic signatures elucidate enhancer-gene relationships that delineate CIMP and non-CIMP colorectal cancers.

Epigenetic changes, like DNA methylation, affect gene expression and in colorectal cancer (CRC), a distinct phenotype called the CpG island methylator phenotype ("CIMP") has significantly higher levels of DNA methylation at so-called "Type C loci" within the genome. We postulate that enhancer-gene pairs are coordinately controlled through DNA methylation in order to regulate the expression of key genes/biomarkers for a particular phenotype.Firstly, we found 24 experimentally-validated enhancers (VISTA enhancer browser) that contained statistically significant (FDR-adjusted q-value of <0.

Promoter profiling and coexpression data analysis identifies 24 novel genes that are coregulated with AMPA receptor genes, GRIAs.

We identified a set of transcriptional elements that are conserved and overrepresented within the promoters of human, mouse, and rat GRIAs by comparing these promoters against a collection of 10,741 gene promoters. Cells regulate functional groups of genes by coordinating the transcriptional and/or posttranscriptional mRNA levels of interacting genes. As such, it is expected that functional groups of genes share the same transcriptional features within their promoters.

Reverse transcriptase template switching and false alternative transcripts.

Reverse transcriptase (RT) can switch from one template to another in a homology-dependent manner. In the study of eukaryotic transcripts, this propensity of RT can produce an artificially deleted cDNA, which can be wrongly interpreted as an alternative transcript. Here, we have investigated the presence of such template-switching artifacts in cDNA databases, by scanning a collection of human splice sites (Information for the Coordinates of Exons, ICE database).

Information for the Coordinates of Exons (ICE): a human splice sites database.

We present a comprehensive database, Information for the Coordinates of Exons (ICE), of genomic splice sites (SSs) for 10,803 human genes. ICE contains 91,846 pairs of donor acceptor sites, supported by the alignment of "full-length" human mRNAs (including transcript variants) on human genomic sequences. ICE represents the largest collection of human SSs known to date and provides a significant resource to both molecular biologists and bioinformaticians alike.

Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells.

Background: Estrogens and their receptors are important in human development, physiology and disease. In this study, we utilized an integrated genome-wide molecular and computational approach to characterize the interaction between the activated estrogen receptor (ER) and the regulatory elements of candidate target genes.

Results: Of around 19,000 genes surveyed in this study, we observed 137 ER-regulated genes in T-47D cells, of which only 89 were direct target genes.

Dragon ERE Finder version 2: A tool for accurate detection and analysis of estrogen response elements in vertebrate genomes.

We present a unique program for identification of estrogen response elements (EREs) in genomic DNA and related analyses. The detection algorithm was tested on several large datasets and makes one prediction in 13 300 nt while achieving a sensitivity of 83%. Users can further investigate selected regions around the identified ERE patterns for transcription factor binding sites based on the TRANSFAC database.

FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes.

FIE2 (5' end Information Extraction v2) is a web-based program for easy identification and extraction of nucleotide sequence around the start of genes (promoter region) and their translation initiation site (TIS). Using information provided by the National Center for Biotechnology Information's (NCBI's) LocusLink, FIE2 identifies the 5'-most end of a gene on its respective chromosome based on alignment of a selected set of mRNAs representative of the gene. FIE2 then uses currently available human genome sequence information to extract the desired sequences.

Information and sequence extraction around the 5'-end and translation initiation site of human genes.

FIE (5'-end Information Extraction) is a web-based program designed primarily to extract the sequence of the regions around the 5'-end and around the translation initiation sites for a particular gene, based on information provided by LocusLink.

Computer model for recognition of functional transcription start sites in RNA polymerase II promoters of vertebrates.

This paper introduces a new computer system for recognition of functional transcription start sites (TSSs) in RNA polymerase II promoter regions of vertebrates. This system allows scanning complete vertebrate genomes for promoters with significantly reduced number of false positive predictions. It can be used in the context of gene finding through its recognition of the 5' end of genes.

Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters.

Dragon Promoter Finder (DPF) locates RNA polymerase II promoters in DNA sequences of vertebrates by predicting Transcription Start Site (TSS) positions. DPF's algorithm uses sensors for three functional regions (promoters, exons and introns) and an Artificial Neural Network (ANN). Results on a large and diverse evaluation set indicate that DPF exhibits a superior predicting ability for TSS location compared to three other promoter-finding programs.