Dong X et. al. Modeling gene expression using chromatin features in various cellular contexts 2012/09/29 ENCODE ษڧձ ೋ֊ಊѪ / @dritoshi #encodejp-28 ཧԽֶݚڀॴ ൃੜɾ࠶ੜՊֶ૯߹ݚڀηϯλʔ
Chromatin features ͔ΒҨࢠൃݱ͕༧ଌͰ͖Δ͔? 4ͭͷ͍ 1. Can we reproduce the quantitative relationship between gene expression levels and histone modifications? 2. Does the relationship hold across different human cell lines and between different groups of genes? 3. Do the most predictive chromatin features differ depending on the expression quantification technique used? 4. How well can the chromatin features predict expression levels of RNA from different cell compartments and/or RNA extracted by different
Software ྨճؼͳͲ Calculation of the mean density of chromatin features bigWigSummary: BigWig and BigBed: enabling browsing of large distributed datasets Variable importance relaimpo: Relative importance of regressors in linear models Regression/classification randomForest: Breiman and Cutler's random forests for classification and regression Regression earth: Multivariate Adaptive Regression Spline Models