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Saulo Augusto de Paula Pinto 1, 2 1 Introduction In order to identify a possible common framework of gene expression.

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Presentation on theme: "Saulo Augusto de Paula Pinto 1, 2 1 Introduction In order to identify a possible common framework of gene expression."— Presentation transcript:

1 Saulo Augusto de Paula Pinto 1, 2 {saulo@pucminas.br}saulo@pucminas.br 1 Introduction In order to identify a possible common framework of gene expression in samples of gene expression data, 418 samples that compose 13 NCBI-GEO series generated on the top of Affymetrix GeneChips platform and 31 SAGE Genie libraries were analyzed. 2 Methodology 3 Results Every sample from different organisms follows a exponential-like decay as the expression values diminish, disregarding the technology, the number of distinct sequences in the samples, the organism or tissue kind. An algorithm to find out a weak framework: one that is composed by pairs of genes in which the first element of the pair is always more expressed than the second one in every analyzed sample. 1 Laboratório de Biodados Departamento de Bioquímica e Imunologia Instituto de Ciências Biológicas – UFMG 5 Conclusions The results point to the existence of a gene expression framework of genes that keep their expression sorting through a vast different set of tissues. Part of a weak framework found for 36 human normal tissues samples considering only the 20 most expressed sequences (MESs) from each sample. A directed edge indicates the gene that is most expressed (source) and the least expressed (target). 2 Instituto de Informática PUC MINAS BARREIRO Toward the Identification of a Gene Expression Framework in Different Types of Tissues and Organisms This finding suggests that the sorting of gene expression and not only the genes expressed has a determinant role in the tissues or organism character. Some results are shown for two data series: one of 36 human normal tissues samples and one of 11 A. thaliana tissues (GEO accessions: GSE2361, GSE607). It was found that the expression sorting is kept in such a way that weak framework rate between a pair of samples can be used even to cluster a set of gene expression data samples. Highly physiologically-related tissue pairs like [amygdala, hippocampus] and [prostate, bladder] or sample replicates like [leaf_gh1, leaf_gh2] have as high as 94.7%, 89.7%, and 94.12% of their sequences pairs conserved, respectively. On the other side, in H. sapiens pairs composed of different tissues like those involving bone marrow, liver and the central nervous system tissues keep expression sorting poorly (< 22%). 4 Discussion Considering all 36 H. sapiens tissues together, 28.5% of the 3,064,841 possible pairs were conserved. For A. thaliana stem and flower conserved least (< 47%) and the 11 samples conserved 55.45% (22892007 of 41286376), as expected to a less complex organism with less diversity of tissues. INPUT: a set of samples sorted by the gene expression such that the most expressed gene (sequence) is in the position 0 and the least expressed is in position N-1, where N is the number of genes (sequences) in each sample. OUTPUT: a list of pairs of genes (sequences) in which the first member keeps its expression order relative to the second member in every sample. 1) Chose a reference sample only to build pairs; 2) For each pair of genes [G C, G L ] in the reference sample where G C is more expressed than G L do 2.1) If G C is more expressed than G L in every sample then include the pair [G C, G L ] in the weak framework; else discard the pair. J. Miguel Ortega 1 {miguel@icb.ufmg.br}miguel@icb.ufmg.br Amygdala hippocampus94.7S MuscleSmall Intestine21.5 Caudate Nucleus hippocampus91.2CerebellumLiver21.3 Amygdala Thalamus91.1Small IntestineFetal Brain 20. 8 Amygdala Caudate Nucleus91.0S MuscleCaudate Nucleus20.4 Corpus Spinal Cord90.7HeartSalivary Gland20.1 hippocampus Thalamus90.4PancreasCaudate Nucleus19.6 Caudate Nucleus Thalamus89.8HeartLiver19.3 Prostate Bladder89.7Caudate NucleusFetal Liver19.1 Brain Thalamus89.6S MuscleLiver18.9 Brain Amygdala89.5Salivary GlandCaudate Nucleus18.8 Brain hippocampus89.1Small IntestineCaudate Nucleus18.6 Ovary Bladder88.5Bone MarrowThalamus18.5 Small Intestine Colon88.2Salivary GlandLiver18.1 Thalamus Spinal Cord88.0Fetal BrainLiver17.7 Bladder Breast87.9Salivary GlandBone Marrow17.4 Caudate Nucleus Spinal Cord87.7Caudate NucleusLiver16.4 Caudate Nucleus Corpus87.7Bone MarrowLiver15.0 Cerebellum Brain87.5S MuscleBone Marrow14.1 Bladder Lung87.3HeartBone Marrow12.8 Bladder Trachea87.2Bone MarrowCaudate Nucleus12.1 Support: FAPEMIG


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