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Related Concept Videos

Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...

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Updated: Jun 22, 2026

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
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Published on: July 21, 2014

ChIP-Chip: algorithms for calling binding sites.

X Shirley Liu1, Clifford A Meyer

  • 1Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|June 3, 2009
PubMed
Summary
This summary is machine-generated.

Analyzing genome-wide ChIP-chip data requires tailored statistical methods. This study presents MAT and MA2C software for reliable analysis of Affymetrix, NimbleGen, and Agilent tiling microarray data.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome-wide ChIP-chip assays generate substantial data for studying protein-DNA interactions.
  • Effective statistical analysis is crucial for reliable interpretation of ChIP-chip results.
  • Analysis methods must account for platform-specific characteristics like probe density and control types.

Purpose of the Study:

  • To describe the application of specific software packages for ChIP-chip data analysis.
  • To provide a framework for analyzing data from different microarray platforms.

Main Methods:

  • Utilized the MAT software package for analyzing one-color Affymetrix tiling microarrays.
  • Employed the MA2C software package for analyzing two-color NimbleGen and Agilent tiling microarrays.
  • Focused on statistical analysis tailored to platform-specific features.

Main Results:

  • Demonstrated the utility of MAT and MA2C for processing and analyzing ChIP-chip data.
  • Showcased the adaptability of these methods across different microarray technologies.
  • Enabled reliable identification of protein-DNA binding events.

Conclusions:

  • MAT and MA2C are effective tools for the statistical analysis of ChIP-chip data.
  • Platform-specific considerations are essential for successful ChIP-chip data analysis.
  • These methods facilitate robust interpretation of genome-wide protein-DNA interactions.