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Open Access Research article

Major role for mRNA stability in shaping the kinetics of gene induction

Ran Elkon1*, Eitan Zlotorynski1, Karen I Zeller2 and Reuven Agami13*

Author Affiliations

1 Division of Gene Regulation, The Netherlands Cancer Institute. Plesmanlaan 121, 1066 CX Amsterdam; The Netherlands

2 Division of Hematology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA

3 Center for Biomedical Genetics, The Netherlands

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BMC Genomics 2010, 11:259  doi:10.1186/1471-2164-11-259

Published: 21 April 2010

Additional files

Additional file 1:

Relationship between mRNA stability, response kinetics and genomic transcribed length in ten expression datasets.

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Additional file 2:

Relationship between mRNA stability and kinetics of induction in various datasets (see legend of Figure 2B, Cand Additional file 1).

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Additional file 3:

Core set of early-induced genes.

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Additional file 4:

Examination of the relationship between mRNA stability and kinetics of induction in the IL2 dataset after removing from the analysis the core set of early induced genes. p-value was calculated for the comparison between the distribution of T half-life of early and late induced genes, as done in Additional file 1, but after the removal of the core genes.

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Additional file 5:

Relationship between kinetics of induction and genomic transcribed length. The effect of genomic transcribed length on the response time is evident only at the very early time points (up to 1-2 hrs after stimulation; see legend of Additional file 1).

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Additional file 6:

The core set of early induced genes is characterized by both (a) very short T half-life (mean T1/2 of 0.90 h vs. 6.45 h, in the core and background sets, respectively) and (b) very short genomic transcribed length (mean genomic transcribedlength of 9,474 bp vs. 39,789 bp, in the core and background sets, respectively). P-values (Wilcoxon test) were calculated for the comparison between the core set and a background set which contained all the rest of genes for which T half-life and genomic transcribed length (i.e., CDS and UTRs annotations) data are available.

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Additional file 7:

Relationship between mRNA stability and kinetics of gene repression in various datasets. Deviations from model prediction are much more frequent here than in the analysis of gene induction (compare with Additional file 2).

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