Protein-DNA interactions are involved in many essential biological processes such as transcription, splicing, replication and DNA repair. ChIP-on-chip is a technique that combines chromatin immunoprecipitation with microarray technology (Oberley et al., 2004). This technique is well suited for a comprehensive analysis of transcription factor binding sites, histone modification patterns, and nucleosome occupancy.
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Motif Discovery on Protein Binding Microarray (PBM) data using Hidden Markov Model and Belief Propagation.


Cis-regulatory Element Annotation System
A software tool designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq data. CEAS provides summary statistics on ChIP enrichment in important genomic regions such as...


Algorithms for Calculating Microarray Enrichment
A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment".


A user-friendly software platform for genome-scale detection of known and novel motifs (recurring patterns) in DNA sequences, applicable to a wide range of motif discovery tasks. Amadeus outperforms extant tools and...


This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments.

ChIP-chip: data, model, and analysis

Authors: Zheng, M., Barrera, L.O., Ren, B., and Wu, Y.N.

Abstract: ChIP-chip (or ChIP-on-chip) is a technology for isolation and identification of genomic sites occupied by specific DNA-binding proteins in living...


Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets.


A peak-finding algorithm used to analyze ChIP-chip microarray data.


The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements.


A web-based tool for ChIP data analysis providing summary statistics in graphs and offering several commonly demanded analyses.


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


An unsupervised learning method to find, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data. ChromaSig recovers known patterns associated with transcriptional...


A tool for finding over-representing short DNA motifs (e.g., transcription factor binding motifs) and estimates the Position Frequency Matrix (PFM) directly from word counts. It is designed for the analysis of...


An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.


A web-based application called Cistrome, based on the Galaxy open source framework. In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major categories, from...


ChIP-on-chip Analysis Suite
A standalone software suite which implements optimized ChIP-on-chip data normalization, improved peak detection, as well as quality control reports.


ChIP-on-chip online
A computational tool that allows the user to search, visualise and store different data associated with gene expression.


Visualize and analyze data generated on Illumina array platforms. GenomeStudio supports the primary analysis of microarray data. Performance-optimized tools and a user-friendly graphical interface allow you to quickly...


Hypergeometric Analysis of Tiling-array and SEQuence data
A powerful tool that accurately identifies functional regions of interest (ROIs) on the genome where a genomic signal significantly deviates from the general genome-wide behavior. HATSEQ also includes a number of...


This package uses hidden Ising models to identify enriched genomic regions in ChIP-chip data.


Estimates Loci of Enhanced Significance (LES) in tiling microarray data.


Motif Discovery scan
A computational method that examines the ChIP-array-selected sequences and searches for DNA sequence motifs representing the protein-DNA interaction sites. MDscan combines the advantages of two widely adopted motif...


NimbleGen Tilingarray Analysis Package
It was developed in the process of our own generated NimbleGen tiling array data analysis.


An efficient de novo motif discovery tool for large-scale genomic sequence data. rGADEM provides a complete set of Bioconductor tools for sequence and motif analysis of ChIP-Seq and ChIP-chip data.


This package facilitates the primary analysis of ChIP-chip data.


R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.


Facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling arrays.


A software tool for ChIP-chip peak calling.


An integrated pipeline for the analysis of large scale chromatin-immunoprecipitation (ChIP) data. From the immunoprecipitated sequences, the over-represented motifs are extracted and clustered into position weight...


A comprehensive web application tool for processing ChIP-chip and ChIP-seq data. The web tool includes two different web interfaces: PELT for ChIP-chip, BELT for ChIP-seq, where both were tested on previously...