Outlier Genes as Biomarkers of Breast Cancer Survivability in Time-Series Data

Abstract

Studying gene expression through various time intervals of breast cancer survival may provide new insights into the recovery from the disease. In this work, we propose a hierarchical clustering method to separate dissimilar groups of gene time-series profiles, which have the furthest distances from the rest of the profiles throughout different time intervals. The isolated outliers can be used as potential biomarkers of Breast Cancer survivability. Gene expressions throughout those time points are cubic spline interpolated to create a trending profile for each gene. After universally aligning the profiles to minimize the vertical area between each pair of profiles, we cluster the genes using hierarchical clustering based on minimized vertical distances [1]. An appropriate number of clusters was chosen based on the profile alignment and agglomerative clustering (PAAC) index as well as visual observations of the clusters. Our study suggests that the combination of proper clustering, distance function and index validation for clusters is a suitable model to identify genes as informative biomarkers of breast cancer survivability.