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Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

Piotr J Balwierz1, Piero Carninci2, Carsten O Daub2, Jun Kawai2, Yoshihide Hayashizaki2, Werner Van Belle3, Christian Beisel3 and Erik van Nimwegen1*

Author Affiliations

1 Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056-CH, Basel, Switzerland

2 RIKEN Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan

3 Laboratory of Quantitative Genomics, Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, Mattenstrasse 26, 4058 Basel, Switzerland

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Genome Biology 2009, 10:R79  doi:10.1186/gb-2009-10-7-r79

Published: 22 July 2009

Additional files

Additional data file 1:

Additional results include the Drosophila RNA-seq data, CAGE replicate data, comparison with FANTOM3 clustering, and statistics on the mouse promoterome.

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Open Data

Additional data file 2:

Data for the 56 human CAGE samples, with tissue/cell line name, treatment and accession numbers.

Format: XLS Size: 69KB Download file

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Open Data

Additional data file 3:

Data for the 66 mouse CAGE samples, with tissue/cell line name, treatment and accession numbers.

Format: XLS Size: 96KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data