Open Access Highly Accessed Methodology article

Estimating accuracy of RNA-Seq and microarrays with proteomics

Xing Fu1, Ning Fu1, Song Guo2, Zheng Yan2, Ying Xu2, Hao Hu23, Corinna Menzel3, Wei Chen3*, Yixue Li1, Rong Zeng1 and Philipp Khaitovich24*

Author Affiliations

1 Key lab of Systems Biology, Shanghai Institutes for Biological Sciences, China Academy of Sciences, Shanghai, 200031, PR China

2 Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, PR China

3 Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany

4 Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany

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BMC Genomics 2009, 10:161  doi:10.1186/1471-2164-10-161

Published: 16 April 2009

Additional files

Additional file 1:

Supplementary figures and tables. Additional file 1 contains all supplementary figures and tables. Figure S1 – Correlation between gene expression levels measured by Affymetrix arrays. Figure S2 – Correlation between gene expression levels measured by RNA-Seq. Figure S3 – Correlation between gene expression levels measured by Affymetrix arrays and RNA-Seq at different sequencing depth. Figure S4 – Correlation between protein and mRNA expression levels measured by Affymetrix arrays or RNA-Seq using different ways to compute mRNA expression level. Figure S5 – Correlation between mRNA expression levels measured by Affymetrix arrays or RNA-Seq and protein expression levels in two technical replicates. Table S1 – Sample information. Table S2 – Total numbers of sequences in the four sequencing experiments. Table S3 – Correlations between gene expression levels measured by Affymetrix array and RNA-Seq. Table S4 – Correlation between protein expression levels and mRNA expression levels measured by Affymetrix arrays and RNA-Seq.

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