Predicting Genetic Regulatory Response Using Classification利用分类预测基因调控反应.pptVIP

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2017-03-08 发布于上海
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Predicting Genetic Regulatory Response Using Classification利用分类预测基因调控反应.ppt

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Predicting Genetic Regulatory Response Using Classification利用分类预测基因调控反应

Predicting Genetic Regulatory Response Using Classification Us v. Them (“Them” being Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, and Christina Leslie, in “Predicting Genetic Regulatory Response Using Classification” (2004) The Problem Current studies of gene transcription tend to be descriptive Need for a predictive system – the ability to predict gene regulation for new experiments Rather than determining patterns in sets of genes and conditions, look at underyling causes of those patterns The Important Parts of Genes Experiments Regulation is determined by binding sites (motifs) and regulators (parents) The significance of experiments, then, is how they affect regulators The significance of genes is what motifs they contain Binding Sites and Regulation Discretize gene response into only up-regulated (1), down-regulated(-1), or unchanged (0) A motif is either present (1) or absent (0) A parent is either up-regulated (1), down-regulated (-1), or unchanged (0) Assume (and we need to check with someone who actually knows something about biology on this) that things only happen if motif is present and parent is either up- or down-regulated What our matrix really looks like g = # of genes e = # of experiments p = # of parents m = # of motifs Then we have g*e response values For each response, we have p*m parent/motif combinations For each parent/motif combination, there are three possibilities – present and up-regulated, present and down-regulated, or all those other possibilities where nothing happens Represent these possibilities as a pair of binary variables, one for up and one for down Some Numbers In the paper, the initial dataset had 6110 genes and 173 experiments 354 motifs are considered 475 regulators are considered Set of genes to consider is reduced to only 1411 genes of interest Some More Numbers Only train on genes that are up- or down-regulated Approx. 8% of gene/experiment pairs from the overall sample appear to be, so, assuming this