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Robust computational reconstitution - a new method for the comparative analysis of gene expression in tissues and isolated cell fractions.

Hoffmann M, Pohlers D, Koczan D, Thiesen HJ, Wölfl S, Kinne RW - BMC Bioinformatics (2006)

Bottom Line: Genes that were either regulated (i.e. differentially-expressed in tissue and isolated cell fractions) or robustly-expressed in all patients were identified using different test statistics.Robust Computational Reconstitution uses an intermediate number of robustly-expressed genes to estimate the relative mRNA proportions.This avoids both the exclusive dependence on the robust expression of individual, highly cell type-specific marker genes and the bias towards an equal distribution upon inclusion of all genes for computation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Leibniz Institute for Natural Products Research and Infection Biology - Hans Knöll Institute, Beutenbergstr, 11a, Jena, Germany. martin.hoffmann@hki-jena.de

ABSTRACT

Background: Biological tissues consist of various cell types that differentially contribute to physiological and pathophysiological processes. Determining and analyzing cell type-specific gene expression under diverse conditions is therefore a central aim of biomedical research. The present study compares gene expression profiles in whole tissues and isolated cell fractions purified from these tissues in patients with rheumatoid arthritis and osteoarthritis.

Results: The expression profiles of the whole tissues were compared to computationally reconstituted expression profiles that combine the expression profiles of the isolated cell fractions (macrophages, fibroblasts, and non-adherent cells) according to their relative mRNA proportions in the tissue. The mRNA proportions were determined by trimmed robust regression using only the most robustly-expressed genes (1/3 to 1/2 of all measured genes), i.e. those showing the most similar expression in tissue and isolated cell fractions. The relative mRNA proportions were determined using several different chip evaluation methods, among which the MAS 5.0 signal algorithm appeared to be most robust. The computed mRNA proportions agreed well with the cell proportions determined by immunohistochemistry except for a minor number of outliers. Genes that were either regulated (i.e. differentially-expressed in tissue and isolated cell fractions) or robustly-expressed in all patients were identified using different test statistics.

Conclusion: Robust Computational Reconstitution uses an intermediate number of robustly-expressed genes to estimate the relative mRNA proportions. This avoids both the exclusive dependence on the robust expression of individual, highly cell type-specific marker genes and the bias towards an equal distribution upon inclusion of all genes for computation.

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Related in: MedlinePlus

Computational reconstitution. Schematic view of the gene expression in the synovial tissue (left) and the computationally reconstituted tissue profile (right). The expression of the synovial tissue is composed of the expression of macrophages , fibroblasts , and non-adherent cells . The expression of the whole tissue is measured as the overall expression profile S. The computationally reconstituted tissue profile S* is composed of the measured expression profiles of the isolated cell fractions, i.e. of macrophages M, fibroblasts F, and non-adherent cells N. The relative mRNA proportions pM, pF, and pN are determined by matching the computationally reconstituted profile S* with the measured tissue profile S, The measured expression profiles are enframed using solid lines.
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Figure 1: Computational reconstitution. Schematic view of the gene expression in the synovial tissue (left) and the computationally reconstituted tissue profile (right). The expression of the synovial tissue is composed of the expression of macrophages , fibroblasts , and non-adherent cells . The expression of the whole tissue is measured as the overall expression profile S. The computationally reconstituted tissue profile S* is composed of the measured expression profiles of the isolated cell fractions, i.e. of macrophages M, fibroblasts F, and non-adherent cells N. The relative mRNA proportions pM, pF, and pN are determined by matching the computationally reconstituted profile S* with the measured tissue profile S, The measured expression profiles are enframed using solid lines.

Mentions: The relative mRNA proportions of macrophages (pM), fibroblasts (pF), and non-adherent cells (pN) were determined for each tissue sample by matching the measured synovial tissue expression profile S and the computationally reconstituted expression profile S* = pM M + pF F + pN N, which in turn combines the measured expression profiles of the isolated cell fractions of macrophages (M), fibroblasts (F), and non-adherent cells (N) according to their relative mRNA proportions (Figure 1).


Robust computational reconstitution - a new method for the comparative analysis of gene expression in tissues and isolated cell fractions.

Hoffmann M, Pohlers D, Koczan D, Thiesen HJ, Wölfl S, Kinne RW - BMC Bioinformatics (2006)

Computational reconstitution. Schematic view of the gene expression in the synovial tissue (left) and the computationally reconstituted tissue profile (right). The expression of the synovial tissue is composed of the expression of macrophages , fibroblasts , and non-adherent cells . The expression of the whole tissue is measured as the overall expression profile S. The computationally reconstituted tissue profile S* is composed of the measured expression profiles of the isolated cell fractions, i.e. of macrophages M, fibroblasts F, and non-adherent cells N. The relative mRNA proportions pM, pF, and pN are determined by matching the computationally reconstituted profile S* with the measured tissue profile S, The measured expression profiles are enframed using solid lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1574358&req=5

Figure 1: Computational reconstitution. Schematic view of the gene expression in the synovial tissue (left) and the computationally reconstituted tissue profile (right). The expression of the synovial tissue is composed of the expression of macrophages , fibroblasts , and non-adherent cells . The expression of the whole tissue is measured as the overall expression profile S. The computationally reconstituted tissue profile S* is composed of the measured expression profiles of the isolated cell fractions, i.e. of macrophages M, fibroblasts F, and non-adherent cells N. The relative mRNA proportions pM, pF, and pN are determined by matching the computationally reconstituted profile S* with the measured tissue profile S, The measured expression profiles are enframed using solid lines.
Mentions: The relative mRNA proportions of macrophages (pM), fibroblasts (pF), and non-adherent cells (pN) were determined for each tissue sample by matching the measured synovial tissue expression profile S and the computationally reconstituted expression profile S* = pM M + pF F + pN N, which in turn combines the measured expression profiles of the isolated cell fractions of macrophages (M), fibroblasts (F), and non-adherent cells (N) according to their relative mRNA proportions (Figure 1).

Bottom Line: Genes that were either regulated (i.e. differentially-expressed in tissue and isolated cell fractions) or robustly-expressed in all patients were identified using different test statistics.Robust Computational Reconstitution uses an intermediate number of robustly-expressed genes to estimate the relative mRNA proportions.This avoids both the exclusive dependence on the robust expression of individual, highly cell type-specific marker genes and the bias towards an equal distribution upon inclusion of all genes for computation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Leibniz Institute for Natural Products Research and Infection Biology - Hans Knöll Institute, Beutenbergstr, 11a, Jena, Germany. martin.hoffmann@hki-jena.de

ABSTRACT

Background: Biological tissues consist of various cell types that differentially contribute to physiological and pathophysiological processes. Determining and analyzing cell type-specific gene expression under diverse conditions is therefore a central aim of biomedical research. The present study compares gene expression profiles in whole tissues and isolated cell fractions purified from these tissues in patients with rheumatoid arthritis and osteoarthritis.

Results: The expression profiles of the whole tissues were compared to computationally reconstituted expression profiles that combine the expression profiles of the isolated cell fractions (macrophages, fibroblasts, and non-adherent cells) according to their relative mRNA proportions in the tissue. The mRNA proportions were determined by trimmed robust regression using only the most robustly-expressed genes (1/3 to 1/2 of all measured genes), i.e. those showing the most similar expression in tissue and isolated cell fractions. The relative mRNA proportions were determined using several different chip evaluation methods, among which the MAS 5.0 signal algorithm appeared to be most robust. The computed mRNA proportions agreed well with the cell proportions determined by immunohistochemistry except for a minor number of outliers. Genes that were either regulated (i.e. differentially-expressed in tissue and isolated cell fractions) or robustly-expressed in all patients were identified using different test statistics.

Conclusion: Robust Computational Reconstitution uses an intermediate number of robustly-expressed genes to estimate the relative mRNA proportions. This avoids both the exclusive dependence on the robust expression of individual, highly cell type-specific marker genes and the bias towards an equal distribution upon inclusion of all genes for computation.

Show MeSH
Related in: MedlinePlus