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Báo cáo y học: "Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Minireview cung cấp cho các bạn kiến thức về ngành y đề tài: Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. | Open Access Methods for analyzing deep sequencing expression data constructing the human and mouse promoterome with deepCAGE data Piotr J Balwierz Piero Carninci Carsten O Daub Jun Kawai Yoshihide Hayashizaki Werner Van Belle Christian Beisel and Erik van Nimwegen Addresses Biozentrum University of Basel and Swiss Institute of Bioinformatics Klingelbergstrasse 50 70 4056-CH Basel Switzerland. tRIKEN Omics Science Center RIKEN Yokohama Institute 1-7-22 Suehiro-cho Tsurumi-ku Yokohama Kanagawa 230-0045 Japan. laboratory of Quantitative Genomics Department of Biosystems Science and Engineering Eidgenossische Technische Hochschule Zurich Mattenstrasse 26 4058 Basel Switzerland. Correspondence Erik van Nimwegen. Email erik.vannimwegen@unibas.ch Published 22 July 2009 Genome Biology 2009 10 R79 doi 10.1186 gb-2009- 10-7-r79 The electronic version of this article is the complete one and can be found online at http genomebiology.com 2009 10 7 R79 Received 23 October 2008 Revised 2 March 2009 Accepted 22 July 2009 2009 Balwierz et al. licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License http creativecommons.org licenses by 2.0 which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract With the advent of ultra high-throughput sequencing technologies increasingly researchers are turning to deep sequencing for gene expression studies. Here we present a set of rigorous methods for normalization quantification of noise and co-expression analysis of deep sequencing data. Using these methods on 122 cap analysis of gene expression CAGE samples of transcription start sites we construct genome-wide promoteromes in human and mouse consisting of a three-tiered hierarchy of transcription start sites transcription start clusters and transcription start regions. Background In recent years several technologies have become available that allow