DOI: 10.5061/dryad.h8m74
title: Data from: Genomic region detection via Spatial Convex Clustering

description: Several modern genomic technologies, such as DNA-Methylation arrays,
 measure spatially registered probes that number in the hundreds of
 thousands across multiple chromosomes. The measured probes are by
 themselves less interesting scientifically; instead scientists seek to
 discover biologically interpretable genomic regions comprised of
 contiguous groups of probes which may act as biomarkers of disease or
 serve as a dimension-reducing pre-processing step for downstream analyses.
 In this paper, we introduce an unsupervised feature learning technique
 which maps technological units (probes) to biological units (genomic
 regions) that are common across all subjects. We use ideas from fusion
 penalties and convex clustering to introduce a method for Spatial Convex
 Clustering, or SpaCC. Our method is specifically tailored to detecting
 multi-subject regions of methylation, but we also test our approach on the
 well-studied problem of detecting segments of copy number variation. We
 formulate our method as a convex optimization problem, develop a massively
 parallelizable algorithm to find its solution, and introduce automated
 approaches for handling missing values and determining tuning parameters.
 Through simulation studies based on real methylation and copy number
 variation data, we show that SpaCC exhibits significant performance gains
 relative to existing methods. Finally, we illustrate SpaCC’s advantages as
 a pre-processing technique that reduces large-scale genomics data into a
 smaller number of genomic regions through several cancer epigenetics case
 studies on subtype discovery, network estimation, and epigenetic-wide
 association.
description: TCGA Genomic Data for
 "Genomic Region Detection via Spatial Convex Clustering" -
 Part00Part 00 of TCGA Genomic
 Data.SpaCC_DataPart00.zipTCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" - Part01Part 01 of TCGA Genomic DataSpaCC_DataPart01.zipTCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" Part 02Part 02 for TCGA Genomic DataSpaCC_DataPart02.zipTCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" Part 03Part 03 for TCGA Genomic DataSpaCC_DataPart03.zipTCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" Part 04Part 04 for TCGA Genomic DataSpaCC_DataPart04.zipTCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" Part 05Part 05 for TCGA Genomic DataSpaCC_DataPart05.zipTCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" Part 06Part 06 for TCGA Genomic DataSpaCC_DataPart06.zipTCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" Part 07Part 07 for TCGA Genomic DataSpaCC_DataPart07.zipTCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" Part 08Part 08 for TCGA Genomic DataSpaCC_DataPart08.zip\TCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" Part 09Part 09 for TCGA Genomic DataSpaCC_DataPart09.zipTCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" Part 10Part 10 for TCGA Genomic DataSpaCC_DataPart10.zipTCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" Part 11Part 11 for TCGA Genomic DataSpaCC_DataPart11.zipTCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" Part 12Part 12 for TCGA Genomic DataSpaCC_DataPart12.zipTCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" Part 13Part 13 for TCGA Genomic DataSpaCC_DataPart13.zipTCGA Genomic Data for "Genomic Region Detection via Spatial Convex Clustering" Part 14Part 14 for TCGA Genomic DataSpaCC_DataPart14.zip