MOIRAI: a compact workflow system for CAGE analysis

作者: Akira Hasegawa , Carsten Daub , Piero Carninci , Yoshihide Hayashizaki , Timo Lassmann

DOI: 10.1186/1471-2105-15-144

关键词:

摘要: Background Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends RNAs in biological sample. After mapping, CAGE peak on genome indicates position an active transcriptional start site (TSS) and number reads correspond its level. prominently used both FANTOM ENCODE project but presently there no software package perform essential data processing steps.

参考文章(20)
Anton Nekrutenko, James Taylor, None, Next-generation sequencing data interpretation: enhancing reproducibility and accessibility Nature Reviews Genetics. ,vol. 13, pp. 667- 672 ,(2012) , 10.1038/NRG3305
Norihiro Maeda, Hiromi Nishiyori, Mari Nakamura, Chika Kawazu, Mitsuyoshi Murata, Hiromi Sano, Kengo Hayashida, Shiro Fukuda, Michihira Tagami, Akira Hasegawa, Kayoko Murakami, Kate Schroder, Katharine Irvine, David A. Hume, Yoshihide Hayashizaki, Piero Carninci, Harukazu Suzuki, Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer BioTechniques. ,vol. 45, pp. 95- 97 ,(2008) , 10.2144/000112814
Hazuki Takahashi, Timo Lassmann, Mitsuyoshi Murata, Piero Carninci, 5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing Nature Protocols. ,vol. 7, pp. 542- 561 ,(2012) , 10.1038/NPROT.2012.005
M. Kanamori-Katayama, M. Itoh, H. Kawaji, T. Lassmann, S. Katayama, M. Kojima, N. Bertin, A. Kaiho, N. Ninomiya, C. O. Daub, P. Carninci, A. R. R. Forrest, Y. Hayashizaki, Unamplified cap analysis of gene expression on a single-molecule sequencer Genome Research. ,vol. 21, pp. 1150- 1159 ,(2011) , 10.1101/GR.115469.110
E. Valen, A. Krogh, Y. Hayashizaki, P. Carninci, A. Sandelin, M. C. Frith, A code for transcription initiation in mammalian genomes Genome Research. ,vol. 18, pp. 1- 12 ,(2007) , 10.1101/GR.6831208
Pea Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, Norihiro Maeda, Rieko Oyama, T Ravasi, B Lenhard, C Wells, Rimantas Kodzius, Kazuro Shimokawa, Vladimir B Bajic, SE Brenner, Serge Batalov, ARR Forrest, Mihaela Zavolan, MJ Davis, Laurens G Wilming, V Aidinis, JE Allen, A Ambesi-Impiombato, R Apweiler, Rajith N Aturaliya, TL Bailey, M Bansal, L Baxter, Kirk W Beisel, T Bersano, H Bono, Alistair M Chalk, KP Chiu, V Choudhary, A Christoffels, DR Clutterbuck, ML Crowe, E Dalla, BP Dalrymple, B De Bono, G Della Gatta, Diego di Bernardo, T Down, P Engstrom, M Fagiolini, G Faulkner, CF Fletcher, T Fukushima, M Furuno, S Futaki, M Gariboldi, P Georgii-Hemming, TR Gingeras, Takashi Gojobori, RE Green, S Gustincich, M Harbers, Yutaka Hayashi, TK Hensch, N Hirokawa, D Hill, L Huminiecki, M Iacono, Kazuho Ikeo, A Iwama, T Ishikawa, M Jakt, A Kanapin, Masaru Katoh, Y Kawasawa, Janet Kelso, H Kitamura, Hiroaki Kitano, G Kollias, SPT Krishnan, A Kruger, SK Kummerfeld, IV Kurochkin, LF Lareau, D Lazarevic, L Lipovich, J Liu, S Liuni, S McWilliam, M Madan Babu, M Madera, Luigi Marchionni, Hideo Matsuda, S Matsuzawa, H Miki, F Mignone, S Miyake, K Morris, Salim Mottagui-Tabar, N Mulder, N Nakano, H Nakauchi, P Ng, R Nilsson, S Nishiguchi, S Nishikawa, F Nori, O Ohara, Y Okazaki, V Orlando, KC Pang, WJ Pavan, G Pavesi, G Pesole, Nikolai Petrovsky, S Piazza, J Reed, JF Reid, Brian Z Ring, M Ringwald, B Rost, Y Ruan, Steven L Salzberg, A Sandelin, C Schneider, C Schonbach, K Sekiguchi, Colin AM Semple, S Seno, L Sessa, Y Sheng, Y Shibata, H Shimada, K Shimada, D Silva, B Sinclair, S Sperling, E Stupka, Koji Sugiura, R Sultana, Yoichi Takenaka, K Taki, K Tammoja, SL Tan, S Tang, MS Taylor, J Tegner, SA Teichmann, HR Ueda, E Van Nimwegen, R Verardo, CL Wei, K Yagi, H Yamanishi, E Zabarovsky, S Zhu, None, The Transcriptional Landscape of the Mammalian Genome Science. ,vol. 309, pp. 1559- 1563 ,(2005) , 10.1126/SCIENCE.1112014
T. Lassmann, Y. Hayashizaki, C. O. Daub, TagDust--a program to eliminate artifacts from next generation sequencing data Bioinformatics. ,vol. 25, pp. 2839- 2840 ,(2009) , 10.1093/BIOINFORMATICS/BTP527
Aaron R. Quinlan, Ira M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics. ,vol. 26, pp. 841- 842 ,(2010) , 10.1093/BIOINFORMATICS/BTQ033
Charles Plessy, Nicolas Bertin, Hazuki Takahashi, Roberto Simone, Md Salimullah, Timo Lassmann, Morana Vitezic, Jessica Severin, Signe Olivarius, Dejan Lazarevic, Nadine Hornig, Valerio Orlando, Ian Bell, Hui Gao, Jacqueline Dumais, Philipp Kapranov, Huaien Wang, Carrie A Davis, Thomas R Gingeras, Jun Kawai, Carsten O Daub, Yoshihide Hayashizaki, Stefano Gustincich, Piero Carninci, Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan Nature Methods. ,vol. 7, pp. 528- 534 ,(2010) , 10.1038/NMETH.1470
H. Li, R. Durbin, Fast and accurate short read alignment with Burrows–Wheeler transform Bioinformatics. ,vol. 25, pp. 1754- 1760 ,(2009) , 10.1093/BIOINFORMATICS/BTP324