Bioinformatics Links Directory : Gene Regulation

This section contains links to tools and resources for predicting gene regulation, such as promoter analysis.

Drosophila DNase I footprint database - (Found July 2, 2008 )

Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.
http://www.flyreg.org/

Eponine - (Found July 2, 2008 )

Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy.
http://www.sanger.ac.uk/Users/td2/eponine/

FatiGOplus - (Found July 2, 2008 )

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.
http://babelomics.bioinfo.cipf.es/fatigoplus/cgi-bin/fatigoplus.cgi

CONREAL - (Found July 2, 2008 )

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.
http://conreal.niob.knaw.nl/

CONFAC - (Found July 2, 2008 )

The Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites. Further information from the user allows CONFAC to identify binding sites that are enriched in the promoter regions of gene clusters from microarray analyses when compared to control gene sets.
http://morenolab.whitehead.emory.edu/cgi-bin/confac/login.pl

CompareProspector - (Found July 2, 2008 )

Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.
http://compareprospector.stanford.edu/

BioBayesNet - (Found July 2, 2008 )

BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.
http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/

BioProspector - (Found July 2, 2008 )

Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.
http://robotics.stanford.edu/~xsliu/BioProspector/

CARRIE - (Found July 2, 2008 )

Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.
http://zlab.bu.edu/CARRIE-web

CEAS - (Found July 2, 2008 )

Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.
http://ceas.cbi.pku.edu.cn