Title |
Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data
|
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Published in |
Genome Biology, July 2009
|
DOI | 10.1186/gb-2009-10-7-r79 |
Pubmed ID | |
Authors |
Piotr J Balwierz, Piero Carninci, Carsten O Daub, Jun Kawai, Yoshihide Hayashizaki, Werner Van Belle, Christian Beisel, Erik van Nimwegen |
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. |
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Geographical breakdown
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Germany | 5 | 2% |
Japan | 3 | <1% |
Russia | 3 | <1% |
Sweden | 3 | <1% |
France | 2 | <1% |
Netherlands | 2 | <1% |
Brazil | 2 | <1% |
Other | 14 | 5% |
Unknown | 257 | 83% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 102 | 33% |
Student > Ph. D. Student | 79 | 25% |
Professor > Associate Professor | 28 | 9% |
Student > Master | 27 | 9% |
Professor | 17 | 5% |
Other | 37 | 12% |
Unknown | 21 | 7% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 194 | 62% |
Biochemistry, Genetics and Molecular Biology | 42 | 14% |
Computer Science | 14 | 5% |
Medicine and Dentistry | 14 | 5% |
Engineering | 8 | 3% |
Other | 17 | 5% |
Unknown | 22 | 7% |