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Genetic vehicle comprising majority of lowly expressed genes guides cell fate decision Nature Precedings
Masa Tsuchiya; Vincent Piras; Masaru Tomita; Alessandro Giuliani; Kumar Selvarajoo.
Cells remarkably take a specific differentiation path among the multiple possibilities that can arise through the multi-dimensional regulation of genome activities. Such deterministic processes suggest the existence of cellular attractors. However, the origins and drivers of the attractors still remain elusive. Here we analyzed the temporal neutrophil differentiation microarray data for two different stimuli, dimethyl sulfoxide (DMSO) and all-trans-retinoic acid (atRA), and expressed their collective dynamics by temporal Pearson correlation and mutual information coordinates. We constructed ensemble of the genes which showed reduction of correlation fluctuations following the inverse square root law. Evaluating their temporal probability density...
Tipo: Manuscript Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4401/version/1
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DNA expression microarrays may be the wrong tool to identify biological pathways Nature Precedings
Adrian Mondry; Marie Loh; Alessandro Giuliani.
DNA microarray expression signatures are expected to provide new insights into patho- physiological pathways. Numerous variant statistical methods have been described for each step of the signal analysis. We employed five similar statistical tests on the same data set at the level of gene selection. Inter-test agreement for the identification of biological pathways in BioCarta, KEGG and Reactome was calculated using Cohen’s k- score. The identification of specific biological pathways showed only moderate agreement (0.30 < k < 0.79) between the analysis methods used. Pathways identified by microarrays must be treated cautiously as they vary according to the statistical method used.
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007 URL: http://precedings.nature.com/documents/1036/version/1
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