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A Machine-Vision Approach to Transmission Electron Microscopy Workflows, Results Analysis and Data Management

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An integrated workflow for analysis of ChIP-chip data.

Karin Weigelt¹, Christoph Moehle, Thomas Stempfl

¹Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.

|August 9, 2008

Summary

This summary is machine-generated.

We present an integrated workflow using Genomatix ChipInspector for analyzing transcription factor binding sites. This method simplifies genome-wide promoter profiling and identifies PU.1 regulated genes in macrophages.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

ChIP-chip is valuable for identifying transcription factor target genes genome-wide.
Current ChIP-chip data analysis, promoter identification, and binding site correlation are labor-intensive.

Purpose of the Study:

To introduce an integrated workflow for analyzing promoter tiling arrays using Genomatix ChipInspector.
To compare ChipInspector with open-source tools for identifying PU.1 regulated genes in mouse macrophages.

Main Methods:

Utilized Genomatix ChipInspector for promoter tiling array analysis.
Employed comparative genomics for transcription factor binding site prediction.
Performed pathway and network modeling for biological interpretation.

Main Results:

The integrated workflow significantly streamlines genome-wide promoter profiling.
Successfully identified PU.1 regulated genes in mouse macrophages.
Demonstrated the utility of ChipInspector in analyzing transcription factor-DNA interactions.

Conclusions:

Genomatix ChipInspector offers an efficient solution for ChIP-chip data analysis.
The workflow enhances the identification of in vivo transcription factor binding sites.
Facilitates a deeper understanding of gene regulation through pathway and network analysis.