کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
976006 933070 2010 9 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Including transcription factor information in the superparamagnetic clustering of microarray data
موضوعات مرتبط
مهندسی و علوم پایه ریاضیات فیزیک ریاضی
پیش نمایش صفحه اول مقاله
Including transcription factor information in the superparamagnetic clustering of microarray data
چکیده انگلیسی

In this work, we modify the superparamagnetic clustering algorithm (SPC) by adding an extra weight to the interaction formula that considers which genes are regulated by the same transcription factor. With this modified algorithm which we call SPCTF, we analyze the Spellman et al. microarray data for cell cycle genes in yeast, and find clusters with a higher number of elements compared with those obtained with the SPC algorithm. Some of the incorporated genes by using SPCFT were not detected at first by Spellman et al. but were later identified by other studies, whereas several genes still remain unclassified. The clusters composed by unidentified genes were analyzed with MUSA, the motif finding using an unsupervised approach algorithm, and this allow us to select the clusters whose elements contain cell cycle transcription factor binding sites as clusters worthy of further experimental studies because they would probably lead to new cell cycle genes. Finally, our idea of introducing the available information about transcription factors to optimize the gene classification could be implemented for other distance-based clustering algorithms.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Physica A: Statistical Mechanics and its Applications - Volume 389, Issue 24, 15 December 2010, Pages 5689–5697
نویسندگان
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