About the Authors
- Pär G Engström
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Affiliations Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway , Programme for Genomics and Bioinformatics, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Harukazu Suzuki
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Affiliation Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
- Noriko Ninomiya
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Affiliation Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
- Altuna Akalin
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Affiliation Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway
- Luca Sessa
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Affiliation Dulbecco Telethon Institute, Institute of Genetics and Biophysics CNR, Naples, Italy
- Giovanni Lavorgna
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Affiliation Department of Biological and Technological Research, San Raffaele Scientific Institute, Milan, Italy
- Alessandro Brozzi
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Affiliations Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy , Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy
- Lucilla Luzi
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Affiliations Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy , Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy
- Sin Lam Tan
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Affiliations Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore , South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
- Liang Yang
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Affiliation Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore
- Galih Kunarso
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Affiliation Department of Biological Sciences, National University of Singapore, Singapore
- Edwin Lian-Chong Ng
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Affiliation Chemical and Life Sciences, Nanyang Polytechnic, Singapore
- Serge Batalov
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Affiliation Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- Claes Wahlestedt
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Affiliations Programme for Genomics and Bioinformatics, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden , Scripps Florida, Jupiter, Florida, United States of America
- Chikatoshi Kai
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Affiliation Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
- Jun Kawai
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Affiliations Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan , Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan
- Piero Carninci
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Affiliations Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan , Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan
- Yoshihide Hayashizaki
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Affiliations Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan , Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan
- Christine Wells
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Affiliation School of Biomolecular and Biomedical Science, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, Queensland, Australia
- Vladimir B Bajic
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Affiliations Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore , South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
- Valerio Orlando
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Affiliation Dulbecco Telethon Institute, Institute of Genetics and Biophysics CNR, Naples, Italy
- James F Reid
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Affiliations Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy , Department of Experimental Oncology, Istituto Nazionale per lo Studio e la Cura dei Tumori, Milan, Italy
- Boris Lenhard
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*To whom correspondence should be addressed. E-mail: Boris.Lenhard@bccs.uib.no (BL); lipovich@gis.a-star.edu.sg (LL)
Affiliations Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway , Programme for Genomics and Bioinformatics, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Leonard Lipovich
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*To whom correspondence should be addressed. E-mail: Boris.Lenhard@bccs.uib.no (BL); lipovich@gis.a-star.edu.sg (LL)
Affiliation Genome Institute of Singapore, Singapore
Competing Interests
The authors have declared that no competing interests exist.
Author Contributions
C. Kai, J. Kawai, P. Carninci, and Y. Hayashizaki contributed sequence data and managed the collaborative project together with C. Wahlestedt. P. G. Engström, B. Lenhard, and L. Lipovich compiled the dataset of TUs, pairs, and chains, performed all analyses not specifically mentioned below, and coordinated the work together with C. Wells. P. G. Engström, H. Suzuki, B. Lenhard, and L. Lipovich designed the PCR experiments together with N. Ninomiya, who performed them. L. Lipovich contributed the analyses of positional equivalents and chain conservation with assistance from P. G. Engström, G. Kunarso, and E. L.-C. Ng. The TSS distribution and sequence composition of bidirectional promoters were analyzed by P. G. Engström, A. Akalin, and B. Lenhard. P. G. Engström, L. Luzi, S. Batalov, C. Wells, J. F. Reid, and B. Lenhard performed the microarray data analysis. L. Sessa, G. Lavorgna, and V. Orlando contributed the analysis of homeotic loci. A. Brozzi, S. L. Tan, L. Yang, and V. B. Bajic contributed additional analyses that had to be excluded because of space constraints. P. G. Engström, L. Lipovich, and B. Lenhard designed and wrote the paper, with contributions from H. Suzuki, L. Luzi, V. B. Bajic, V. Orlando, and J. F. Reid.