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GREAT
Predicts functions of cis-regulatory regions. Many coding genes are well annotated with their biological functions. Non-coding regions typically lack such annotation. GREAT assigns biological meaning to a set of non-coding genomic regions by analyzing the annotations of the nearby genes. Thus, it is particularly useful in studying cis functions of sets of non-coding genomic regions. Cis-regulatory regions can be identified via both experimental methods (e.g. ChIP-seq) and by computational methods (e.g. comparative genomics).
TIP / Target Identification from Profiles
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Identifies Transcription Factor (TF) target genes based on ChIP-seq or ChIP-chip data. The TIP model provides a gene list ranked by the regulatory potential by the TF and gives a confidence score, which allows the user to select a subset of genes for creation of testable hypothesis and further experimental investigation. With ever-increasing genomic occupation data, the model provides a powerful tool for understanding gene regulation.
CISMAPPER
Predicts the regulatory targets of a transcription factor (TF) using the correlation between a histone mark at the TF’s bound sites and the expression of each gene across a panel of tissues. CISMAPPER provides a method that is more accurate than simple distance-based methods, but that places a minimum burden on the user to provide auxiliary data. It uses only data for a single histone modification and gene expression across a small panel of tissues. The use of CISMAPPER need not be restricted to the analysis of TF ChIP-seq data.
ChIP-PED
Predicts biological contexts in which a transcription factor (TF) and its target genes are functionally active. ChIP-PED is a software which allows users to extend the scope of their ChIPx data to possibly novel biological systems without performing additional costly and time-consuming ChIPx experiments. Given a TF and its activated and repressed target genes defined using ChIPx and gene expression data in one or more biological contexts, the software searches for other contexts in which the TF is likely to be functionally active.
BART / Binding Analysis for Regulation of Transcription
New
Predicts transcription factors whose genomic binding profile correlates with query cis-regulatory regions to regulate gene expression in human or mouse genomes. BART is based on a curated union DNaseI hypersensitive sites (UDHS) used as a repertoire of all cis-regulatory regions in the genome. This software offers functional interpretations to differential gene expression analysis and can be applied to validate knock-down or knock-out experiments.
ChIPXpress
Aims to improve identification of transcription factor (TF) target gene from ChIP-seq and ChIP-chip data using publicly available gene expression profiles. ChIPXpress is an R package that uses regulatory information from the diverse cell types, tissues, and diseases in publicly available gene expression data (PED) to enhance functional TF target gene prediction from ChIPx data. The software was developed using two large compendiums of human and mouse gene expression profiles collected from GEO.
Target Explorer
Obsolete
Allows users to create customized libraries of transcription factor (TF) binding site matrices based on user-defined sets of training sequences. Target Explorer is an online application including a search function for clusters of binding sites for specified sets of TFs. It also assists users in the extraction of annotation for potential target genes regulated by a specified set of TFs. This tool is specifically designed for the well-annotated D. melanogaster genome.
cisTargetX
Obsolete
Identifies the correct motif from a set of co-expressed genes and predicts target genes of individual Transcription Factors (TFs). cisTargetX uses statistical correlations between co-expressed gene sets and genome-wide target prioritizations on the basis of rankings of conserved motif cluster predictions. It can determine whether a set of candidate genes, for example a mixture of direct and indirect target genes, is enriched for direct targets of a certain TF or combination of TFs.
TF Target Mapper
Obsolete
Allows users to Transcription Factors (TF) Target Genes. TF Target Mapper in a BLAST search tool that aims to distinguish extract annotated information in chromatin immunoprecipitated sequences and to facilitate large sequence data collections from ChIP experiments analysis. It integrates several functionalities such as pattern recognition for specific transcription factor binding sites or options for cleaning and filtering sequences from vector and repetitive elements.
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