TileMap: Create chromosomal map of tiling array hybridizations

Hong Kai Ji, Wing Hung Wong

Research output: Contribution to journalArticle

Abstract

Motivation: Tiling array is a new type of microarray that can be used to survey genomic transcriptional activities and transcription factor binding sites at high resolution. The goal of this paper is to develop effective statistical tools to identify genomic loci that show transcriptional or protein binding patterns of interest. Results: A two-step approach is proposed and is implemented in TileMap. In the first step, a test-statistic is computed for each probe based on a hierarchical empirical Bayes model. In the second step, the test-statistics of probes within a genomic region are used to infer whether the region is of interest or not. Hierarchical empirical Bayes model shrinks variance estimates and increases sensitivity of the analysis. It allows complex multiple sample comparisons that are essential for the study of temporal and spatial patterns of hybridization across different experimental conditions. Neighboring probes are combined through a moving average method (MA) or a hidden Markov model (HMM). Unbalanced mixture subtraction is proposed to provide approximate estimates of false discovery rate for MA and model parameters for HMM.

Original languageEnglish (US)
Pages (from-to)3629-3636
Number of pages8
JournalBioinformatics
Volume21
Issue number18
DOIs
StatePublished - Sep 15 2005
Externally publishedYes

Fingerprint

Tiling
Exercise Test
Hierarchical Bayes
Genomics
Empirical Bayes
Probe
Moving Average
Hidden Markov models
Markov Model
Test Statistic
Protein Binding
Statistics
Transcription factors
Transcription Factors
Binding Sites
Spatial Pattern
Binding sites
Subtraction
Microarrays
Transcription Factor

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

TileMap : Create chromosomal map of tiling array hybridizations. / Ji, Hong Kai; Wong, Wing Hung.

In: Bioinformatics, Vol. 21, No. 18, 15.09.2005, p. 3629-3636.

Research output: Contribution to journalArticle

Ji, Hong Kai ; Wong, Wing Hung. / TileMap : Create chromosomal map of tiling array hybridizations. In: Bioinformatics. 2005 ; Vol. 21, No. 18. pp. 3629-3636.
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