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Target gene detection 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…
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GREAT
Web

GREAT

Predicts functions of cis-regulatory regions. Many coding genes are well…

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…

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ChIP-BIT
Desktop

ChIP-BIT Bayesian Inference of Target genes using ChIP-seq profiles

A Bayesian approach to reliably detect transcription factor binding sites…

A Bayesian approach to reliably detect transcription factor binding sites (TFBSs) and their target genes by jointly modeling binding signal intensities and binding locations of TFBSs. Specifically, a…

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BETA
Desktop

BETA Binding and Expression Target Analysis

A software package that integrates ChIP-seq of transcription factors or…

A software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes.

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CCAT
Desktop

CCAT Combinatorial Code Analysis Tool

A software package for predicting genome-wide co-binding between biological…

A software package for predicting genome-wide co-binding between biological regulators such as Transcription factors (TFs).

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CISMAPPER
Desktop

CISMAPPER

Predicts the regulatory targets of a transcription factor (TF) using the…

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.…

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CREB Target…
Dataset

CREB Target Gene Database

Compiles information about cAMP-response element binding protein (CREB) target…

Compiles information about cAMP-response element binding protein (CREB) target genes. CREB Target Gene Database intends to furnish, for each entry, CREB binding sites on the promoters and their…

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ChIPXpress
Desktop

ChIPXpress

A R package designed to improve ChIP-seq and ChIP-chip target gene ranking…

A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data.

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TargetCaller
Desktop

TargetCaller

A systematic evaluation of computational methods for defining TF targets based…

A systematic evaluation of computational methods for defining TF targets based on ChIP-seq data.

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ChIP-PED
Desktop

ChIP-PED

Predicts biological contexts in which a transcription factor (TF) and its…

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…

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iTAR
Web
Desktop

iTAR

Supports target gene identification in seven species, ranging from yeast to…

Supports target gene identification in seven species, ranging from yeast to human. To facilitate investigating the quality of ChIP-seq/ChIP-chip data, the iTAR web server generates the chart of the…

DynaMO
Desktop

DynaMO dynamic motif occupancy

Predicts important transcription factors (TFs) and their binding sites…

Predicts important transcription factors (TFs) and their binding sites responsible for dynamic processes. DynaMO uses global chromatin profiling data from a dynamic process and TF binding motifs as…

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TIP
Desktop

TIP Target Identification from Profiles

Identifies Transcription Factor (TF) target genes based on ChIP-seq or…

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,…

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TF2LncRNA
Web

TF2LncRNA

Based on ChIP-Seq peak lists of transcription factors (TFs) from ENCODE and…

Based on ChIP-Seq peak lists of transcription factors (TFs) from ENCODE and annotated human lncRNAs from GENCODE, a web-based interface was developed where TF peaks from each ChIP-Seq experiment are…

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TFBphylo
Desktop

TFBphylo

An R package implementing a phylogenetic tree based method to model the on/off…

An R package implementing a phylogenetic tree based method to model the on/off rates of transcription factor binding (TFB) events, and uses the EM algorithm to estimate model parameters.

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TF Target…
Desktop

TF Target Mapper

Allows users to Transcription Factors (TF) Target Genes. TF Target Mapper in a…

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…

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