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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Combinatorial Gene Control02:33

Combinatorial Gene Control

Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
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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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ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect

Jing Qin1, Mulin Jun Li, Panwen Wang

  • 1Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong SAR, China.

Nucleic Acids Research
|May 19, 2011
PubMed
Summary

This study introduces ChIP-Array, a web server integrating Chromatin Immunoprecipitation (ChIP-X) and gene expression data. It helps identify direct and indirect target genes regulated by transcription factors (TFs) across multiple species.

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Published on: July 7, 2010

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Chromatin Immunoprecipitation (ChIP-X) methods like ChIP-Seq and ChIP-chip map transcription factor binding sites (TFBS).
  • Microarray analysis measures gene expression changes but cannot distinguish direct from indirect TF targets.
  • Both ChIP-X and microarray methods can yield false positives, complicating TF function analysis.

Purpose of the Study:

  • To develop a web server, ChIP-Array, that integrates ChIP-X and gene expression data.
  • To enable more effective analysis of transcription factor binding sites (TFBS) and target gene identification.
  • To assist in the functional characterization of transcription factors (TFs).

Main Methods:

  • Integration of ChIP-X data (ChIP-Seq, ChIP-chip) with microarray expression profiling data.
  • Development of a web server accessible for human, mouse, yeast, fruit fly, and Arabidopsis data.
  • Utilizing combined data to differentiate direct and indirect target genes regulated by TFs.

Main Results:

  • ChIP-Array successfully integrates ChIP-X and expression data from multiple model organisms.
  • The server facilitates the identification of direct and indirect target genes of transcription factors.
  • Provides a unified platform for analyzing TF regulatory networks.

Conclusions:

  • The ChIP-Array web server offers a novel approach to TFBS analysis by combining ChIP-X and expression data.
  • It aids researchers in understanding TF function and regulatory mechanisms.
  • This integrated approach reduces false positives and enhances the accuracy of target gene identification.