About the Authors

Pär G Engström

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

Affiliation Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan

Noriko Ninomiya

Affiliation Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan

Altuna Akalin

Affiliation Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway

Luca Sessa

Affiliation Dulbecco Telethon Institute, Institute of Genetics and Biophysics CNR, Naples, Italy

Giovanni Lavorgna

Affiliation Department of Biological and Technological Research, San Raffaele Scientific Institute, Milan, Italy

Alessandro Brozzi

Affiliations Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy , Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy

Lucilla Luzi

Affiliations Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy , Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy

Sin Lam Tan

Affiliations Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore , South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa

Liang Yang

Affiliation Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore

Galih Kunarso

Affiliation Department of Biological Sciences, National University of Singapore, Singapore

Edwin Lian-Chong Ng

Affiliation Chemical and Life Sciences, Nanyang Polytechnic, Singapore

Serge Batalov

Affiliation Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America

Claes Wahlestedt

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

Affiliation Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan

Jun Kawai

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

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

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

Affiliation School of Biomolecular and Biomedical Science, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, Queensland, Australia

Vladimir B Bajic

Affiliations Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore , South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa

Valerio Orlando

Affiliation Dulbecco Telethon Institute, Institute of Genetics and Biophysics CNR, Naples, Italy

James F Reid

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

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

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.