Target gene identification software tools | ChIP sequencing data analysis
Chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) has great potential for elucidating transcriptional networks, by measuring genome-wide binding of transcription factors (TFs) at high resolution. Despite the precision of these experiments, identification of genes directly regulated by a TF (target genes) is not trivial.
Provides a range of functionalities for ChIP data analyses. CisGenome allows visualization, data normalization, peak detection, false discovery rate (FDR) computation, gene-peak association, and sequence and motif analysis. The software can handle data from two types of designs common in ChIP-seq experiments. The basic functionalities of CisGenome can be used in combination to address several different biological questions.
Allows analysis of factor binding and differential expression in mammalian genomes. BETA has three main functions: (i) to predict whether a factor has activating or repressive function; (ii) to infer the factor’s target genes and (iii) to identify the binding motif of the factor and its collaborators, which might modulate the factor’s activating or repressive function.
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.
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.
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.
A pipeline for the identification of transcription factor target genes. TargetOrtho uses experimentally derived consensus-binding sites together with an alignment-free assignment of conservation. TargetOrtho offers a complementary approach to existing software that focuses mainly on de novo motif discovery by instead beginning with an experimentally validated motif and searching for conserved regulatory target genes.
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.