Open Access Highly Accessed Research article

Correlations between RNA and protein expression profiles in 23 human cell lines

Marcus Gry12, Rebecca Rimini1, Sara Strömberg2, Anna Asplund2, Fredrik Pontén2, Mathias Uhlén1 and Peter Nilsson1*

Author Affiliations

1 Department of Proteomics, School of Biotechnology, AlbaNova University Center, KTH – Royal Institute of Technology, S-10691 Stockholm, Sweden

2 Department of Genetics & Pathology, Rudbeck Laboratory, Uppsala University Hospital, S-75185 Uppsala, Sweden

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BMC Genomics 2009, 10:365  doi:10.1186/1471-2164-10-365

Published: 7 August 2009

Additional files

Additional file 1:

Cell line summary. Description of the cell lines used in the experiments.

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Additional file 2:

Effect of missing values on the mean correlation coefficient. Effects on the mean correlation coefficient of applying different filtration criteria, i.e. the number of allowed missing values (0 – 23) in the RNA oligo assay data. The x-axis indicates the number of missing values and the y-axis the mean correlation value. The numbers in the plot indicate the number of remaining data points. The mean correlations, post-filtration, range from 0.214 to 0.237.

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Additional file 3:

Number of replicate probes and antibodies. Histograms of gene product probes/antibodies replicates used to measure expression levels of the Ensembl gene ID products identified by each platform. The values are averaged across the cell lines whenever replicate hits are found.

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Additional file 4:

Summary of correlation coefficients. Details of the 169 Ensembl gene IDs for which strong correlations were found in comparisons of data obtained from all three platforms, and the correlation coefficients obtained.

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Additional file 5:

Summary of the biological processes ontology results. Table showing results from the Biological Process gene enrichment analysis. Each category (Gene ontology term), and the total number of members from the dataset within each category are listed. The expected number within each category, the numbers of members derived from the dataset, and the associated p values (both unadjusted and adjusted using a false discovery rate multiple adjustment method) are also presented. The category name column contains keywords for the respective categories.

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Additional file 6:

Summary of the cellular compartment ontology results. Table showing results from the Cellular Compartment gene enrichment analysis. Each category (Gene ontology term), and the total number of members from the data set within each category are listed. The expected number within each category, the numbers of members derived from the dataset, and the associated p values (both unadjusted and adjusted using a false discovery rate multiple adjustment method) are also presented. The category name column contains keywords for the respective categories.

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Additional file 7:

Dendrograms based on hierarchical clustering of the complete dataset. Dendrograms from hierarchical clustering based on 1066 genes, using the same clustering procedure as for the smaller subset of 167 Ensembl gene IDs.

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Additional file 8:

Summary of the array versus RT-PCR results. (A) Correlations between Oligo array and RT-PCR data (middle column) and the array and protein data (right column). (B) Correlations between cDNA array and RT-PCR data (middle column) and the array and protein data (right column. (C) Correlation between RT-PCR data and the immunoassay data. A "-" sign correspond to a missing value.

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Additional file 9:

Linear relationship between correlation coefficients from array and RT-PCR intensity signals. Linear regression of the correlations between the oligo microarray data and the cDNA microarray data (y-axis) and the correlations between each of the array data assays and the RT-PCR assay data (x-axis). The slope is significantly positive (p-value 0.01).

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