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A new projection method for biological semantic map generation

Journal of Biomedical Science and Engineering 2010年第1期3卷 13-19页

作者： Hoan N. Nguyen Nicolas Wicker david kieffer Olivier Poch 不详

Low-dimensional representation is a convenient method of obtaining a synthetic view of complex datasets and has been used in various domains for a long time. When the representation is related to words in a document, this kind of representation is also called a semantic map. The two most popular methods are self-organizing maps and generative topographic mapping. The second approach is statistically well-founded but far less computationally efficient than the first. On the other hand, a drawback of self-organizing maps is that they do not project all points, but only map nodes. This paper presents a method of obtaining the projections for all data points complementary to the self-organizing map nodes. The idea is to project points so that their initial distances to some cluster centers are as conserved as possible. The method is tested on an oil flow dataset and then applied to a large protein sequence dataset described by keywords. It has been integrated into an interactive data browser for biological databases.

关键词： Semantic Map Dimension Reduction Biological Database SOM

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TCP14 and TCP15 Mediate the Promotion of Seed Germination by Gibberellins in Arabidopsis thaliana

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Molecular Plant 2015年第3期8卷 482-485页

作者： Francesca Resentini Amelia Felipo-Benavent Lucia Colombo Miguel A. Blázquez david Alabadí Simona Masiero Dipartimento di Bioscienze Università. degli Studi di Milano via Celoria 26 20133 Milano Italy Instituto de Biologfa Molecular y Celular de Plantas (CSIC-Universidacl Politécnica de Valencia) Ingeniero Fausto Elio sin 46022 Valencia Spain

Dear Editor,Seed germination is a major developmental transition in a plant＇s life that involves the concerted action of several genetic and physiological pathways （Holdsworth et al., 2008）, and mostly consists of the resumption of embryo growth after a long quiescence imposed during seed maturation. In mature seeds, germination is repressed by abscisic acid （ABA）, while favorable environmental conditions promote gibberellin （GA） biosynthesis and decrease ABA （Holdsworth et al., 2008）. The increase in GA levels is essential for the rupture of testa and endosperm （Lee et al., 2002）. The activation of cell division in the embryo is an integral part of germination that precedes the protrusion of the root through the seed coat. In Arabidopsis, this activation has been linked to significant early changes in the expression of cell-cycle elements （Masubelele et al., 2005）. In the root apical meristem （RAM）, GAs regulate cell divisions （Achard et al., 2009; 0beda-Tomás et al., 2009）. Similarly, the transcription factors （TFs） TEOSINTE BRANCHED1/ CYCLOIDEA/PROLIFERATING CELL FACTOR14 （TCP14） and TCP15 have been proposed to regulate cell proliferation （kieffer et al., 2011）. Moreover, the activity of TCP14 is necessary to undergo seed germination and, remarkably, seeds lacking this activity are hypersensitive to the negative effects on germination of GA biosynthesis inhibitor paclobutrazol, suggesting a functional relationship between this TF and GAs （Tatematsu et al., 2008）. Taking these observations into account, we hypothesized that TCP14 and TCP15 mediate GA-dependent activation of the cell cycle during germination.

关键词：赤霉素类分生组织萌芽内皮缩血管肽类拟南芥属细胞分裂胰岛素种子

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