Including transcription factor information in the superparamagnetic clustering of microarray data

Details Including transcription factor information in the superparamagnetic clustering of microarray data Including transcription factor information in the superparamagnetic clustering of microarray data

2010-12-22

arxiv.org/abs/1012.5063v1

Physica A 389(24), 5689-5697 (2010)

Biology

Quantitative Biology

Molecular Networks

16 pages, 6 Figures made of a total of 11 figures, 2 tables, supplementary info file containing a list of the 27 most stable c

Scientific paper

10.1016/j.physa.2010.09.006

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 that we call SPCTF, we analyze 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 worth of further experimental studies because they would probably lead to new cell cycle genes. Finally, our idea of introducing available information about transcription factors to optimize the gene classification could be implemented for other distance-based clustering algorithms

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