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Open Access Highly Accessed Methodology article

Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees

Donna M Toleno1, Gabriel Renaud2, Tyra G Wolfsberg2, Munirul Islam3, Derek E Wildman3, Kimberly D Siegmund4 and Joseph G Hacia1*

Author Affiliations

1 Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA

2 National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA

3 Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA

4 Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA

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BMC Bioinformatics 2009, 10:77  doi:10.1186/1471-2105-10-77

Published: 5 March 2009

Additional files

Additional file 1:

Effects of probe number on the variation of gene expression scores. The relationships between probe number and the interquartile ranges of human gene expression scores are provided.

Format: PPT Size: 178KB Download file

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Additional file 2:

Effects of probe number on the variation of gene expression scores. The relationships between probe number and the interquartile ranges of chimpanzee gene expression scores are provided.

Format: PPT Size: 178KB Download file

This file can be viewed with: Microsoft PowerPoint Viewer

Open Data

Additional file 3:

Rates of evolution for U133Plus2 microarray probe sets based on their corresponding single RefSeq ID. The rates of evolution for U133Plus2 microarray probe sets based on their corresponding single RefSeq ID are provided.

Format: XLS Size: 7MB Download file

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Additional file 4:

Relationships between numbers of probes remaining after masking and rates of evolution. The relationships between the number of 1H_1C probes in a probe set and the rates of evolution of corresponding RefSeqs are provided.

Format: PPT Size: 125KB Download file

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Additional file 5:

Comparative analysis of inferred differential expression based on masked and unmasked data sets. Venn diagrams summarizing the relationships of probe sets showing differential expression based on masked and unmasked data sets.

Format: PPT Size: 69KB Download file

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Additional file 6:

Instructions for the application of masks for the analysis of human and chimpanzee gene expression data obtained from Affymetrix U133Plus2 microarrays. We provide instructions for the application of masks for the analysis of human and chimpanzee data obtained from Affymetrix U133Plus2 gene expression microarrays.

Format: DOC Size: 76KB Download file

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Additional file 7:

Master mask file. This is the master mask file that can be applied for cross-species gene expression analyses according to the instructions provided in Additional File 6.

Format: TXT Size: 1.4MB Download file

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