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15 results on '"Ruan, Yijun"'

1. Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons

Author

Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Ministry of Science and Higher Education (Poland), European Commission, Fundació La Marató de TV3, Generalitat Valenciana, Fundación la Caixa, National Institutes of Health (US), Human Frontier Science Program, Consejo Superior de Investigaciones Científicas (España), Blanco, Beatriz del, Niñerola, Sergio, Martín-Gonzalez, Ana M., Paraíso-Luna, Juan, Kim, Minji, Muñoz-Viana, Rafael, Racovac, Carina, Sánchez-Mut, José Vicente, Ruan, Yijun, Barco, Ángel, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Ministry of Science and Higher Education (Poland), European Commission, Fundació La Marató de TV3, Generalitat Valenciana, Fundación la Caixa, National Institutes of Health (US), Human Frontier Science Program, Consejo Superior de Investigaciones Científicas (España), Blanco, Beatriz del, Niñerola, Sergio, Martín-Gonzalez, Ana M., Paraíso-Luna, Juan, Kim, Minji, Muñoz-Viana, Rafael, Racovac, Carina, Sánchez-Mut, José Vicente, Ruan, Yijun, and Barco, Ángel

Abstract

Kdm1a is a histone demethylase linked to intellectual disability with essential roles during gastrulation and the terminal differentiation of specialized cell types, including neurons, that remains highly expressed in the adult brain. To explore Kdm1a’s function in adult neurons, we develop inducible and forebrain-restricted Kdm1a knockouts. By applying multi-omic transcriptome, epigenome and chromatin conformation data, combined with super-resolution microscopy, we find that Kdm1a elimination causes the neuronal activation of nonneuronal genes that are silenced by the polycomb repressor complex and interspersed with active genes. Functional assays demonstrate that the N-terminus of Kdm1a contains an intrinsically disordered region that is essential to segregate Kdm1a-repressed genes from the neighboring active chromatin environment. Finally, we show that the segregation of Kdm1a-target genes is weakened in neurons during natural aging, underscoring the role of Kdm1a safeguarding neuronal genome organization and gene silencing throughout life.

Published
2024

2. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project

Author

Dekker, Job, Dekker, Job, Alber, Frank, Aufmkolk, Sarah, Beliveau, Brian J, Bruneau, Benoit G, Belmont, Andrew S, Bintu, Lacramioara, Boettiger, Alistair, Calandrelli, Riccardo, Disteche, Christine M, Gilbert, David M, Gregor, Thomas, Hansen, Anders S, Huang, Bo, Huangfu, Danwei, Kalhor, Reza, Leslie, Christina S, Li, Wenbo, Li, Yun, Ma, Jian, Noble, William S, Park, Peter J, Phillips-Cremins, Jennifer E, Pollard, Katherine S, Rafelski, Susanne M, Ren, Bing, Ruan, Yijun, Shav-Tal, Yaron, Shen, Yin, Shendure, Jay, Shu, Xiaokun, Strambio-De-Castillia, Caterina, Vertii, Anastassiia, Zhang, Huaiying, Zhong, Sheng, Dekker, Job, Dekker, Job, Alber, Frank, Aufmkolk, Sarah, Beliveau, Brian J, Bruneau, Benoit G, Belmont, Andrew S, Bintu, Lacramioara, Boettiger, Alistair, Calandrelli, Riccardo, Disteche, Christine M, Gilbert, David M, Gregor, Thomas, Hansen, Anders S, Huang, Bo, Huangfu, Danwei, Kalhor, Reza, Leslie, Christina S, Li, Wenbo, Li, Yun, Ma, Jian, Noble, William S, Park, Peter J, Phillips-Cremins, Jennifer E, Pollard, Katherine S, Rafelski, Susanne M, Ren, Bing, Ruan, Yijun, Shav-Tal, Yaron, Shen, Yin, Shendure, Jay, Shu, Xiaokun, Strambio-De-Castillia, Caterina, Vertii, Anastassiia, Zhang, Huaiying, and Zhong, Sheng

Abstract

The four-dimensional nucleome (4DN) consortium studies the architecture of the genome and the nucleus in space and time. We summarize progress by the consortium and highlight the development of technologies for (1) mapping genome folding and identifying roles of nuclear components and bodies, proteins, and RNA, (2) characterizing nuclear organization with time or single-cell resolution, and (3) imaging of nuclear organization. With these tools, the consortium has provided over 2,000 public datasets. Integrative computational models based on these data are starting to reveal connections between genome structure and function. We then present a forward-looking perspective and outline current aims to (1) delineate dynamics of nuclear architecture at different timescales, from minutes to weeks as cells differentiate, in populations and in single cells, (2) characterize cis-determinants and trans-modulators of genome organization, (3) test functional consequences of changes in cis- and trans-regulators, and (4) develop predictive models of genome structure and function.

Published
2023

3. An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity

Author

Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Closser, Michael, Guo, Yuchun, Wang, Ping, Patel, Tulsi, Jang, Sumin, Hammelman, Jennifer, De Nooij, Joriene C, Kopunova, Rachel, Mazzoni, Esteban O, Ruan, Yijun, Gifford, David K, Wichterle, Hynek, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Closser, Michael, Guo, Yuchun, Wang, Ping, Patel, Tulsi, Jang, Sumin, Hammelman, Jennifer, De Nooij, Joriene C, Kopunova, Rachel, Mazzoni, Esteban O, Ruan, Yijun, Gifford, David K, and Wichterle, Hynek

Abstract

Proper assembly and function of the nervous system requires the generation of a uniquely diverse population of neurons expressing a cell-type-specific combination of effector genes that collectively define neuronal morphology, connectivity, and function. How countless partially overlapping but cell-type-specific patterns of gene expression are controlled at the genomic level remains poorly understood. Here we show that neuronal genes are associated with highly complex gene regulatory systems composed of independent cell-type- and cell-stage-specific regulatory elements that reside in expanded non-coding genomic domains. Mapping enhancer-promoter interactions revealed that motor neuron enhancers are broadly distributed across the large chromatin domains. This distributed regulatory architecture is not a unique property of motor neurons but is employed throughout the nervous system. The number of regulatory elements increased dramatically during the transition from invertebrates to vertebrates, suggesting that acquisition of new enhancers might be a fundamental process underlying the evolutionary increase in cellular complexity.

Published
2023

4. An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells

Author

Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Zhang, Zhizhuo, Chng, Kern Rei, Lingadahalli, Shreyas, Chen, Zikai, Liu, Mei Hui, Do, Huy Hoang, Cai, Shaojiang, Rinaldi, Nicola, Poh, Huay Mei, Li, Guoliang, Sung, Ying Ying, Heng, Charlie L., Core, Leighton J., Tan, Si Kee, Ruan, Xiaoan, Lis, John T., Kellis, Manolis, Ruan, Yijun, Sung, Wing-Kin, Cheung, Edwin, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Zhang, Zhizhuo, Chng, Kern Rei, Lingadahalli, Shreyas, Chen, Zikai, Liu, Mei Hui, Do, Huy Hoang, Cai, Shaojiang, Rinaldi, Nicola, Poh, Huay Mei, Li, Guoliang, Sung, Ying Ying, Heng, Charlie L., Core, Leighton J., Tan, Si Kee, Ruan, Xiaoan, Lis, John T., Kellis, Manolis, Ruan, Yijun, Sung, Wing-Kin, and Cheung, Edwin

Abstract

The aberrant activities of transcription factors such as the androgen receptor (AR) underpin prostate cancer development. While the AR cis-regulation has been extensively studied in prostate cancer, information pertaining to the spatial architecture of the AR transcriptional circuitry remains limited. In this paper, we propose a novel framework to profile long-range chromatin interactions associated with AR and its collaborative transcription factor, erythroblast transformation-specific related gene (ERG), using chromatin interaction analysis by paired-end tag (ChIA-PET). We identified ERG-associated long-range chromatin interactions as a cooperative component in the AR-associated chromatin interactome, acting in concert to achieve coordinated regulation of a subset of AR target genes. Through multifaceted functional data analysis, we found that AR-ERG interaction hub regions are characterized by distinct functional signatures, including bidirectional transcription and cotranscription factor binding. In addition, cancer-associated long noncoding RNAs were found to be connected near protein-coding genes through AR-ERG looping. Finally, we found strong enrichment of prostate cancer genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) at AR-ERG co-binding sites participating in chromatin interactions and gene regulation, suggesting GWAS target genes identified from chromatin looping data provide more biologically relevant findings than using the nearest gene approach. Taken together, our results revealed an ARERG- centric higher-order chromatin structure that drives coordinated gene expression in prostate cancer progression and the identification of potential target genes for therapeutic intervention.

Published
2020

5. Highlights from the 11th ISCB Student Council Symposium 2015: Dublin, Ireland. 10 July 2015

Author

Wilkins, Katie, Hassan, Mehedi, Francescatto, Margherita, Jespersen, Jakob, Parra, R. Gonzalo, Cuypers, Bart, DeBlasio, Dan, Junge, Alexander, Jigisha, Anupama, Rahman, Farzana, Laenen, Griet, Willems, Sander, Thorrez, Lieven, Moreau, Yves, Raju, Nagarajan, Chothani, Sonia Pankaj, Ramakrishnan, C., Sekijima, Masakazu, Gromiha, M. Michael, Slator, Paddy J, Burroughs, Nigel J, Szałaj, Przemysław, Tang, Zhonghui, Michalski, Paul, Luo, Oskar, Li, Xingwang, Ruan, Yijun, Plewczynski, Dariusz, Fiscon, Giulia, Weitschek, Emanuel, Ciccozzi, Massimo, Bertolazzi, Paola, Felici, Giovanni, Meysman, Pieter, Vanaerschot, Manu, Berg, Maya, Imamura, Hideo, Dujardin, Jean-Claude, Laukens, Kris, Domanova, Westa, Krycer, James R., Chaudhuri, Rima, Yang, Pengyi, Vafaee, Fatemeh, Fazakerley, Daniel J., Humphrey, Sean J., James, David E., Kuncic, Zdenka, Wilkins, Katie, Hassan, Mehedi, Francescatto, Margherita, Jespersen, Jakob, Parra, R. Gonzalo, Cuypers, Bart, DeBlasio, Dan, Junge, Alexander, Jigisha, Anupama, Rahman, Farzana, Laenen, Griet, Willems, Sander, Thorrez, Lieven, Moreau, Yves, Raju, Nagarajan, Chothani, Sonia Pankaj, Ramakrishnan, C., Sekijima, Masakazu, Gromiha, M. Michael, Slator, Paddy J, Burroughs, Nigel J, Szałaj, Przemysław, Tang, Zhonghui, Michalski, Paul, Luo, Oskar, Li, Xingwang, Ruan, Yijun, Plewczynski, Dariusz, Fiscon, Giulia, Weitschek, Emanuel, Ciccozzi, Massimo, Bertolazzi, Paola, Felici, Giovanni, Meysman, Pieter, Vanaerschot, Manu, Berg, Maya, Imamura, Hideo, Dujardin, Jean-Claude, Laukens, Kris, Domanova, Westa, Krycer, James R., Chaudhuri, Rima, Yang, Pengyi, Vafaee, Fatemeh, Fazakerley, Daniel J., Humphrey, Sean J., James, David E., and Kuncic, Zdenka

Abstract

A1 Highlights from the eleventh ISCB Student Council Symposium 2015

Published
2016

6. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations.

Author

Zhang, Yubo, Zhang, Yubo, Wong, Chee-Hong, Birnbaum, Ramon Y, Li, Guoliang, Favaro, Rebecca, Ngan, Chew Yee, Lim, Joanne, Tai, Eunice, Poh, Huay Mei, Wong, Eleanor, Mulawadi, Fabianus Hendriyan, Sung, Wing-Kin, Nicolis, Silvia, Ahituv, Nadav, Ruan, Yijun, Wei, Chia-Lin, Zhang, Yubo, Zhang, Yubo, Wong, Chee-Hong, Birnbaum, Ramon Y, Li, Guoliang, Favaro, Rebecca, Ngan, Chew Yee, Lim, Joanne, Tai, Eunice, Poh, Huay Mei, Wong, Eleanor, Mulawadi, Fabianus Hendriyan, Sung, Wing-Kin, Nicolis, Silvia, Ahituv, Nadav, Ruan, Yijun, and Wei, Chia-Lin

Abstract

In multicellular organisms, transcription regulation is one of the central mechanisms modelling lineage differentiation and cell-fate determination. Transcription requires dynamic chromatin configurations between promoters and their corresponding distal regulatory elements. It is believed that their communication occurs within large discrete foci of aggregated RNA polymerases termed transcription factories in three-dimensional nuclear space. However, the dynamic nature of chromatin connectivity has not been characterized at the genome-wide level. Here, through a chromatin interaction analysis with paired-end tagging approach using an antibody that primarily recognizes the pre-initiation complexes of RNA polymerase II, we explore the transcriptional interactomes of three mouse cells of progressive lineage commitment, including pluripotent embryonic stem cells, neural stem cells and neurosphere stem/progenitor cells. Our global chromatin connectivity maps reveal approximately 40,000 long-range interactions, suggest precise enhancer-promoter associations and delineate cell-type-specific chromatin structures. Analysis of the complex regulatory repertoire shows that there are extensive colocalizations among promoters and distal-acting enhancers. Most of the enhancers associate with promoters located beyond their nearest active genes, indicating that the linear juxtaposition is not the only guiding principle driving enhancer target selection. Although promoter-enhancer interactions exhibit high cell-type specificity, promoters involved in interactions are found to be generally common and mostly active among different cells. Chromatin connectivity networks reveal that the pivotal genes of reprogramming functions are transcribed within physical proximity to each other in embryonic stem cells, linking chromatin architecture to coordinated gene expression. Our study sets the stage for the full-scale dissection of spatial and temporal genome structures and their roles in orche

Published
2013

7. Landscape of transcription in human cells.

Author

Djebali, Sarah, Djebali, Sarah, Davis, Carrie A, Merkel, Angelika, Dobin, Alex, Lassmann, Timo, Mortazavi, Ali, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Schlesinger, Felix, Xue, Chenghai, Marinov, Georgi K, Khatun, Jainab, Williams, Brian A, Zaleski, Chris, Rozowsky, Joel, Röder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F, Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T, Bar, Nadav S, Batut, Philippe, Bell, Kimberly, Bell, Ian, Chakrabortty, Sudipto, Chen, Xian, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jacqueline, Duttagupta, Radha, Falconnet, Emilie, Fastuca, Meagan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J, Gao, Hui, Gonzalez, David, Gordon, Assaf, Gunawardena, Harsha, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Luo, Oscar J, Park, Eddie, Persaud, Kimberly, Preall, Jonathan B, Ribeca, Paolo, Risk, Brian, Robyr, Daniel, Sammeth, Michael, Schaffer, Lorian, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Wrobel, John, Yu, Yanbao, Ruan, Xiaoan, Hayashizaki, Yoshihide, Harrow, Jennifer, Gerstein, Mark, Hubbard, Tim, Reymond, Alexandre, Antonarakis, Stylianos E, Hannon, Gregory, Giddings, Morgan C, Ruan, Yijun, Wold, Barbara, Carninci, Piero, Guigó, Roderic, Gingeras, Thomas R, Djebali, Sarah, Djebali, Sarah, Davis, Carrie A, Merkel, Angelika, Dobin, Alex, Lassmann, Timo, Mortazavi, Ali, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Schlesinger, Felix, Xue, Chenghai, Marinov, Georgi K, Khatun, Jainab, Williams, Brian A, Zaleski, Chris, Rozowsky, Joel, Röder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F, Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T, Bar, Nadav S, Batut, Philippe, Bell, Kimberly, Bell, Ian, Chakrabortty, Sudipto, Chen, Xian, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jacqueline, Duttagupta, Radha, Falconnet, Emilie, Fastuca, Meagan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J, Gao, Hui, Gonzalez, David, Gordon, Assaf, Gunawardena, Harsha, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Luo, Oscar J, Park, Eddie, Persaud, Kimberly, Preall, Jonathan B, Ribeca, Paolo, Risk, Brian, Robyr, Daniel, Sammeth, Michael, Schaffer, Lorian, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Wrobel, John, Yu, Yanbao, Ruan, Xiaoan, Hayashizaki, Yoshihide, Harrow, Jennifer, Gerstein, Mark, Hubbard, Tim, Reymond, Alexandre, Antonarakis, Stylianos E, Hannon, Gregory, Giddings, Morgan C, Ruan, Yijun, Wold, Barbara, Carninci, Piero, Guigó, Roderic, and Gingeras, Thomas R

Abstract

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

Published
2012

8. Landscape of transcription in human cells.

Author

Djebali, Sarah, Djebali, Sarah, Davis, Carrie A, Merkel, Angelika, Dobin, Alex, Lassmann, Timo, Mortazavi, Ali, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Schlesinger, Felix, Xue, Chenghai, Marinov, Georgi K, Khatun, Jainab, Williams, Brian A, Zaleski, Chris, Rozowsky, Joel, Röder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F, Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T, Bar, Nadav S, Batut, Philippe, Bell, Kimberly, Bell, Ian, Chakrabortty, Sudipto, Chen, Xian, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jacqueline, Duttagupta, Radha, Falconnet, Emilie, Fastuca, Meagan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J, Gao, Hui, Gonzalez, David, Gordon, Assaf, Gunawardena, Harsha, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Luo, Oscar J, Park, Eddie, Persaud, Kimberly, Preall, Jonathan B, Ribeca, Paolo, Risk, Brian, Robyr, Daniel, Sammeth, Michael, Schaffer, Lorian, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Wrobel, John, Yu, Yanbao, Ruan, Xiaoan, Hayashizaki, Yoshihide, Harrow, Jennifer, Gerstein, Mark, Hubbard, Tim, Reymond, Alexandre, Antonarakis, Stylianos E, Hannon, Gregory, Giddings, Morgan C, Ruan, Yijun, Wold, Barbara, Carninci, Piero, Guigó, Roderic, Gingeras, Thomas R, Djebali, Sarah, Djebali, Sarah, Davis, Carrie A, Merkel, Angelika, Dobin, Alex, Lassmann, Timo, Mortazavi, Ali, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Schlesinger, Felix, Xue, Chenghai, Marinov, Georgi K, Khatun, Jainab, Williams, Brian A, Zaleski, Chris, Rozowsky, Joel, Röder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F, Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T, Bar, Nadav S, Batut, Philippe, Bell, Kimberly, Bell, Ian, Chakrabortty, Sudipto, Chen, Xian, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jacqueline, Duttagupta, Radha, Falconnet, Emilie, Fastuca, Meagan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J, Gao, Hui, Gonzalez, David, Gordon, Assaf, Gunawardena, Harsha, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Luo, Oscar J, Park, Eddie, Persaud, Kimberly, Preall, Jonathan B, Ribeca, Paolo, Risk, Brian, Robyr, Daniel, Sammeth, Michael, Schaffer, Lorian, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Wrobel, John, Yu, Yanbao, Ruan, Xiaoan, Hayashizaki, Yoshihide, Harrow, Jennifer, Gerstein, Mark, Hubbard, Tim, Reymond, Alexandre, Antonarakis, Stylianos E, Hannon, Gregory, Giddings, Morgan C, Ruan, Yijun, Wold, Barbara, Carninci, Piero, Guigó, Roderic, and Gingeras, Thomas R

Abstract

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

Published
2012

9. International network of cancer genome projects

Author

Hudson, Thomas J., Anderson, Warwick, Aretz, Axel, Barker, Anna D., Bell, Cindy, Bernabe, Rosa R., Bhan, M. K., Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S., Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M., Jennings, Jennifer L., Kerr, David, Klatt, Peter, Kolar, Patrik, Kusuda, Jun, Lane, David P., Laplace, Frank, Lu, Youyong, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, T. S., Remacle, Jacques, Schafer, Alan J., Shibata, Tatsuhiro, Stratton, Michael R., Vockley, Joseph G., Watanabe, Koichi, Yang, Huanming, Yuen, Matthew M. F., Knoppers, M., Bobrow, Martin, Cambon-Thomsen, Anne, Dressler, Lynn G., Dyke, Stephanie O. M., Joly, Yann, Kato, Kazuto, Kennedy, Karen L., Nicolas, Pilar, Parker, Michael J., Rial-Sebbag, Emmanuelle, Romeo-Casabona, Carlos M., Shaw, Kenna M., Wallace, Susan, Wiesner, Georgia L., Zeps, Nikolajs, Lichter, Peter, Biankin, Andrew V., Chabannon, Christian, Chin, Lynda, Clement, Bruno, de Alava, Enrique, Degos, Francoise, Ferguson, Martin L., Geary, Peter, Hayes, D. Neil, Johns, Amber L., Nakagawa, Hidewaki, Penny, Robert, Piris, Miguel A., Sarin, Rajiv, Scarpa, Aldo, van de Vijver, Marc, Futreal, P. Andrew, Aburatani, Hiroyuki, Bayes, Monica, Bowtell, David D. L., Campbell, Peter J., Estivill, Xavier, Grimmond, Sean M., Gut, Ivo, Hirst, Martin, Lopez-Otin, Carlos, Majumder, Partha, Marra, Marco, Ning, Zemin, Puente, Xose S., Ruan, Yijun, Stunnenberg, Hendrik G., Swerdlow, Harold, Velculescu, Victor E., Wilson, Richard K., Xue, Hong H., Yang, Liu, Spellman, Paul T., Bader, Gary D., Boutros, Paul C., Flicek, Paul, Getz, Gad, Guigo, Roderic, Guo, Guangwu, Haussler, David, Heath, Simon, Hubbard, Tim J., Jiang, Tao, Jones, Steven M., Li, Qibin, Lopez-Bigas, Nuria, Luo, Ruibang, Pearson, John V., Quesada, Victor, Raphael, Benjamin J., Sander, Chris, Speed, Terence P., Stuart, Joshua M., Teague, Jon W., Totoki, Yasushi, Tsunoda, Tatsuhiko, Valencia, Alfonso, Wheeler, David A., Wu, Honglong, Zhao, Shancen, Zhou, Guangyu, Stein, Lincoln D., Lathrop, Mark, Ouellette, B. F. Francis, Thomas, Gilles, Yoshida, Teruhiko, Axton, Myles, Gunter, Chris, McPherson, John D., Miller, Linda J., Kasprzyk, Arek, Zhang, Junjun, Haider, Syed A., Wang, Jianxin, Yung, Christina K., Cros, Anthony, Liang, Yong, Gnaneshan, Saravanamuttu, Guberman, Jonathan, Hsu, Jack, Chalmers, Don R. C., Hasel, Karl W., Kaan, Terry S. H., Knoppers, Bartha M., Lowrance, William W., Masui, Tohru, Rodriguez, Laura Lyman, Vergely, Catherine, Cloonan, Nicole, Defazio, Anna, Eshleman, James R., Etemadmoghadam, Dariush, Gardiner, Brooke B., Kench, James G., Sutherland, Robert L., Tempero, Margaret A., Waddell, Nicola J., Wilson, Peter J., Gallinger, Steve, Tsao, Ming-Sound, Shaw, Patricia A., Petersen, Gloria M., Mukhopadhyay, Debabrata, DePinho, Ronald A., Thayer, Sarah, Muthuswamy, Lakshmi, Shazand, Kamran, Beck, Timothy, Sam, Michelle, Timms, Lee, Ballin, Vanessa, Ji, Jiafu, Zhang, Xiuqing, Chen, Feng, Hu, Xueda, Yang, Qi, Tian, Geng, Zhang, Lianhai, Xing, Xiaofang, Li, Xianghong, Zhu, Zhenggang, Yu, Yingyan, Yu, Jun, Tost, Joerg, Brennan, Paul, Holcatova, Ivana, Zaridze, David, Brazma, Alvis, Egevad, Lars, Prokhortchouk, Egor, Banks, Rosamonde Elizabeth, Uhlén, Mathias, Viksna, Juris, Pontén, Fredrik, Skryabin, Konstantin, Birney, Ewan, Borg, Ake, Borresen-Dale, Anne-Lise, Caldas, Carlos, Foekens, John A., Martin, Sancha, Reis-Filho, Jorge S., Richardson, Andrea L., Sotiriou, Christos, van't Veer, Laura, Birnbaum, Daniel, Blanche, Helene, Boucher, Pascal, Boyault, Sandrine, Masson-Jacquemier, Jocelyne D., Pauporte, Iris, Pivot, Xavier, Vincent-Salomon, Anne, Tabone, Eric, Theillet, Charles, Treilleux, Isabelle, Bioulac-Sage, Paulette, Decaens, Thomas, Franco, Dominique, Gut, Marta, Samuel, Didier, Zucman-Rossi, Jessica, Eils, Roland, Brors, Benedikt, Korbel, Jan O., Korshunov, Andrey, Landgraf, Pablo, Lehrach, Hans, Pfister, Stefan, Radlwimmer, Bernhard, Reifenberger, Guido, Taylor, Michael D., von Kalle, Christof, Majumder, Partha P., Pederzoli, Paolo, Lawlor, Rita T., Delledonne, Massimo, Bardelli, Alberto, Gress, Thomas, Klimstra, David, Zamboni, Giuseppe, Nakamura, Yusuke, Miyano, Satoru, Fujimoto, Akihiro, Campo, Elias, de Sanjose, Silvia, Montserrat, Emili, Gonzalez-Diaz, Marcos, Jares, Pedro, Himmelbauer, Heinz, Bea, Silvia, Aparicio, Samuel, Easton, Douglas F., Collins, Francis S., Compton, Carolyn C., Lander, Eric S., Burke, Wylie, Green, Anthony R., Hamilton, Stanley R., Kallioniemi, Olli P., Ley, Timothy J., Liu, Edison T., Wainwright, Brandon J., Hudson, Thomas J., Anderson, Warwick, Aretz, Axel, Barker, Anna D., Bell, Cindy, Bernabe, Rosa R., Bhan, M. K., Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S., Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M., Jennings, Jennifer L., Kerr, David, Klatt, Peter, Kolar, Patrik, Kusuda, Jun, Lane, David P., Laplace, Frank, Lu, Youyong, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, T. S., Remacle, Jacques, Schafer, Alan J., Shibata, Tatsuhiro, Stratton, Michael R., Vockley, Joseph G., Watanabe, Koichi, Yang, Huanming, Yuen, Matthew M. F., Knoppers, M., Bobrow, Martin, Cambon-Thomsen, Anne, Dressler, Lynn G., Dyke, Stephanie O. M., Joly, Yann, Kato, Kazuto, Kennedy, Karen L., Nicolas, Pilar, Parker, Michael J., Rial-Sebbag, Emmanuelle, Romeo-Casabona, Carlos M., Shaw, Kenna M., Wallace, Susan, Wiesner, Georgia L., Zeps, Nikolajs, Lichter, Peter, Biankin, Andrew V., Chabannon, Christian, Chin, Lynda, Clement, Bruno, de Alava, Enrique, Degos, Francoise, Ferguson, Martin L., Geary, Peter, Hayes, D. Neil, Johns, Amber L., Nakagawa, Hidewaki, Penny, Robert, Piris, Miguel A., Sarin, Rajiv, Scarpa, Aldo, van de Vijver, Marc, Futreal, P. Andrew, Aburatani, Hiroyuki, Bayes, Monica, Bowtell, David D. L., Campbell, Peter J., Estivill, Xavier, Grimmond, Sean M., Gut, Ivo, Hirst, Martin, Lopez-Otin, Carlos, Majumder, Partha, Marra, Marco, Ning, Zemin, Puente, Xose S., Ruan, Yijun, Stunnenberg, Hendrik G., Swerdlow, Harold, Velculescu, Victor E., Wilson, Richard K., Xue, Hong H., Yang, Liu, Spellman, Paul T., Bader, Gary D., Boutros, Paul C., Flicek, Paul, Getz, Gad, Guigo, Roderic, Guo, Guangwu, Haussler, David, Heath, Simon, Hubbard, Tim J., Jiang, Tao, Jones, Steven M., Li, Qibin, Lopez-Bigas, Nuria, Luo, Ruibang, Pearson, John V., Quesada, Victor, Raphael, Benjamin J., Sander, Chris, Speed, Terence P., Stuart, Joshua M., Teague, Jon W., Totoki, Yasushi, Tsunoda, Tatsuhiko, Valencia, Alfonso, Wheeler, David A., Wu, Honglong, Zhao, Shancen, Zhou, Guangyu, Stein, Lincoln D., Lathrop, Mark, Ouellette, B. F. Francis, Thomas, Gilles, Yoshida, Teruhiko, Axton, Myles, Gunter, Chris, McPherson, John D., Miller, Linda J., Kasprzyk, Arek, Zhang, Junjun, Haider, Syed A., Wang, Jianxin, Yung, Christina K., Cros, Anthony, Liang, Yong, Gnaneshan, Saravanamuttu, Guberman, Jonathan, Hsu, Jack, Chalmers, Don R. C., Hasel, Karl W., Kaan, Terry S. H., Knoppers, Bartha M., Lowrance, William W., Masui, Tohru, Rodriguez, Laura Lyman, Vergely, Catherine, Cloonan, Nicole, Defazio, Anna, Eshleman, James R., Etemadmoghadam, Dariush, Gardiner, Brooke B., Kench, James G., Sutherland, Robert L., Tempero, Margaret A., Waddell, Nicola J., Wilson, Peter J., Gallinger, Steve, Tsao, Ming-Sound, Shaw, Patricia A., Petersen, Gloria M., Mukhopadhyay, Debabrata, DePinho, Ronald A., Thayer, Sarah, Muthuswamy, Lakshmi, Shazand, Kamran, Beck, Timothy, Sam, Michelle, Timms, Lee, Ballin, Vanessa, Ji, Jiafu, Zhang, Xiuqing, Chen, Feng, Hu, Xueda, Yang, Qi, Tian, Geng, Zhang, Lianhai, Xing, Xiaofang, Li, Xianghong, Zhu, Zhenggang, Yu, Yingyan, Yu, Jun, Tost, Joerg, Brennan, Paul, Holcatova, Ivana, Zaridze, David, Brazma, Alvis, Egevad, Lars, Prokhortchouk, Egor, Banks, Rosamonde Elizabeth, Uhlén, Mathias, Viksna, Juris, Pontén, Fredrik, Skryabin, Konstantin, Birney, Ewan, Borg, Ake, Borresen-Dale, Anne-Lise, Caldas, Carlos, Foekens, John A., Martin, Sancha, Reis-Filho, Jorge S., Richardson, Andrea L., Sotiriou, Christos, van't Veer, Laura, Birnbaum, Daniel, Blanche, Helene, Boucher, Pascal, Boyault, Sandrine, Masson-Jacquemier, Jocelyne D., Pauporte, Iris, Pivot, Xavier, Vincent-Salomon, Anne, Tabone, Eric, Theillet, Charles, Treilleux, Isabelle, Bioulac-Sage, Paulette, Decaens, Thomas, Franco, Dominique, Gut, Marta, Samuel, Didier, Zucman-Rossi, Jessica, Eils, Roland, Brors, Benedikt, Korbel, Jan O., Korshunov, Andrey, Landgraf, Pablo, Lehrach, Hans, Pfister, Stefan, Radlwimmer, Bernhard, Reifenberger, Guido, Taylor, Michael D., von Kalle, Christof, Majumder, Partha P., Pederzoli, Paolo, Lawlor, Rita T., Delledonne, Massimo, Bardelli, Alberto, Gress, Thomas, Klimstra, David, Zamboni, Giuseppe, Nakamura, Yusuke, Miyano, Satoru, Fujimoto, Akihiro, Campo, Elias, de Sanjose, Silvia, Montserrat, Emili, Gonzalez-Diaz, Marcos, Jares, Pedro, Himmelbauer, Heinz, Bea, Silvia, Aparicio, Samuel, Easton, Douglas F., Collins, Francis S., Compton, Carolyn C., Lander, Eric S., Burke, Wylie, Green, Anthony R., Hamilton, Stanley R., Kallioniemi, Olli P., Ley, Timothy J., Liu, Edison T., and Wainwright, Brandon J.

Abstract

The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies., QC 20110114

Published
2010
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10. International network of cancer genome projects.

Author

International Cancer Genome Consortium, International Cancer Genome Consortium, Hudson, Thomas J, Anderson, Warwick, Artez, Axel, Barker, Anna D, Bell, Cindy, Bernabé, Rosa R, Bhan, MK, Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S, Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M, Jennings, Jennifer L, Kerr, David, Klatt, Peter, Kolar, Patrik, Kusada, Jun, Lane, David P, Laplace, Frank, Youyong, Lu, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, TS, Remacle, Jacques, Schafer, Alan J, Shibata, Tatsuhiro, Stratton, Michael R, Vockley, Joseph G, Watanabe, Koichi, Yang, Huanming, Yuen, Matthew MF, Knoppers, Bartha M, Bobrow, Martin, Cambon-Thomsen, Anne, Dressler, Lynn G, Dyke, Stephanie OM, Joly, Yann, Kato, Kazuto, Kennedy, Karen L, Nicolás, Pilar, Parker, Michael J, Rial-Sebbag, Emmanuelle, Romeo-Casabona, Carlos M, Shaw, Kenna M, Wallace, Susan, Wiesner, Georgia L, Zeps, Nikolajs, Lichter, Peter, Biankin, Andrew V, Chabannon, Christian, Chin, Lynda, Clément, Bruno, de Alava, Enrique, Degos, Françoise, Ferguson, Martin L, Geary, Peter, Hayes, D Neil, Johns, Amber L, Kasprzyk, Arek, Nakagawa, Hidewaki, Penny, Robert, Piris, Miguel A, Sarin, Rajiv, Scarpa, Aldo, van de Vijver, Marc, Futreal, P Andrew, Aburatani, Hiroyuki, Bayés, Mónica, Botwell, David DL, Campbell, Peter J, Estivill, Xavier, Grimmond, Sean M, Gut, Ivo, Hirst, Martin, López-Otín, Carlos, Majumder, Partha, Marra, Marco, McPherson, John D, Ning, Zemin, Puente, Xose S, Ruan, Yijun, Stunnenberg, Hendrik G, Swerdlow, Harold, Velculescu, Victor E, Wilson, Richard K, Xue, Hong H, Yang, Liu, Spellman, Paul T, Bader, Gary D, Boutros, Paul C, International Cancer Genome Consortium, International Cancer Genome Consortium, Hudson, Thomas J, Anderson, Warwick, Artez, Axel, Barker, Anna D, Bell, Cindy, Bernabé, Rosa R, Bhan, MK, Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S, Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M, Jennings, Jennifer L, Kerr, David, Klatt, Peter, Kolar, Patrik, Kusada, Jun, Lane, David P, Laplace, Frank, Youyong, Lu, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, TS, Remacle, Jacques, Schafer, Alan J, Shibata, Tatsuhiro, Stratton, Michael R, Vockley, Joseph G, Watanabe, Koichi, Yang, Huanming, Yuen, Matthew MF, Knoppers, Bartha M, Bobrow, Martin, Cambon-Thomsen, Anne, Dressler, Lynn G, Dyke, Stephanie OM, Joly, Yann, Kato, Kazuto, Kennedy, Karen L, Nicolás, Pilar, Parker, Michael J, Rial-Sebbag, Emmanuelle, Romeo-Casabona, Carlos M, Shaw, Kenna M, Wallace, Susan, Wiesner, Georgia L, Zeps, Nikolajs, Lichter, Peter, Biankin, Andrew V, Chabannon, Christian, Chin, Lynda, Clément, Bruno, de Alava, Enrique, Degos, Françoise, Ferguson, Martin L, Geary, Peter, Hayes, D Neil, Johns, Amber L, Kasprzyk, Arek, Nakagawa, Hidewaki, Penny, Robert, Piris, Miguel A, Sarin, Rajiv, Scarpa, Aldo, van de Vijver, Marc, Futreal, P Andrew, Aburatani, Hiroyuki, Bayés, Mónica, Botwell, David DL, Campbell, Peter J, Estivill, Xavier, Grimmond, Sean M, Gut, Ivo, Hirst, Martin, López-Otín, Carlos, Majumder, Partha, Marra, Marco, McPherson, John D, Ning, Zemin, Puente, Xose S, Ruan, Yijun, Stunnenberg, Hendrik G, Swerdlow, Harold, Velculescu, Victor E, Wilson, Richard K, Xue, Hong H, Yang, Liu, Spellman, Paul T, Bader, Gary D, and Boutros, Paul C

Abstract

The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

Published
2010

11. International network of cancer genome projects.

Author

International Cancer Genome Consortium, International Cancer Genome Consortium, Hudson, Thomas J, Anderson, Warwick, Artez, Axel, Barker, Anna D, Bell, Cindy, Bernabé, Rosa R, Bhan, MK, Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S, Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M, Jennings, Jennifer L, Kerr, David, Klatt, Peter, Kolar, Patrik, Kusada, Jun, Lane, David P, Laplace, Frank, Youyong, Lu, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, TS, Remacle, Jacques, Schafer, Alan J, Shibata, Tatsuhiro, Stratton, Michael R, Vockley, Joseph G, Watanabe, Koichi, Yang, Huanming, Yuen, Matthew MF, Knoppers, Bartha M, Bobrow, Martin, Cambon-Thomsen, Anne, Dressler, Lynn G, Dyke, Stephanie OM, Joly, Yann, Kato, Kazuto, Kennedy, Karen L, Nicolás, Pilar, Parker, Michael J, Rial-Sebbag, Emmanuelle, Romeo-Casabona, Carlos M, Shaw, Kenna M, Wallace, Susan, Wiesner, Georgia L, Zeps, Nikolajs, Lichter, Peter, Biankin, Andrew V, Chabannon, Christian, Chin, Lynda, Clément, Bruno, de Alava, Enrique, Degos, Françoise, Ferguson, Martin L, Geary, Peter, Hayes, D Neil, Johns, Amber L, Kasprzyk, Arek, Nakagawa, Hidewaki, Penny, Robert, Piris, Miguel A, Sarin, Rajiv, Scarpa, Aldo, van de Vijver, Marc, Futreal, P Andrew, Aburatani, Hiroyuki, Bayés, Mónica, Botwell, David DL, Campbell, Peter J, Estivill, Xavier, Grimmond, Sean M, Gut, Ivo, Hirst, Martin, López-Otín, Carlos, Majumder, Partha, Marra, Marco, McPherson, John D, Ning, Zemin, Puente, Xose S, Ruan, Yijun, Stunnenberg, Hendrik G, Swerdlow, Harold, Velculescu, Victor E, Wilson, Richard K, Xue, Hong H, Yang, Liu, Spellman, Paul T, Bader, Gary D, Boutros, Paul C, International Cancer Genome Consortium, International Cancer Genome Consortium, Hudson, Thomas J, Anderson, Warwick, Artez, Axel, Barker, Anna D, Bell, Cindy, Bernabé, Rosa R, Bhan, MK, Calvo, Fabien, Eerola, Iiro, Gerhard, Daniela S, Guttmacher, Alan, Guyer, Mark, Hemsley, Fiona M, Jennings, Jennifer L, Kerr, David, Klatt, Peter, Kolar, Patrik, Kusada, Jun, Lane, David P, Laplace, Frank, Youyong, Lu, Nettekoven, Gerd, Ozenberger, Brad, Peterson, Jane, Rao, TS, Remacle, Jacques, Schafer, Alan J, Shibata, Tatsuhiro, Stratton, Michael R, Vockley, Joseph G, Watanabe, Koichi, Yang, Huanming, Yuen, Matthew MF, Knoppers, Bartha M, Bobrow, Martin, Cambon-Thomsen, Anne, Dressler, Lynn G, Dyke, Stephanie OM, Joly, Yann, Kato, Kazuto, Kennedy, Karen L, Nicolás, Pilar, Parker, Michael J, Rial-Sebbag, Emmanuelle, Romeo-Casabona, Carlos M, Shaw, Kenna M, Wallace, Susan, Wiesner, Georgia L, Zeps, Nikolajs, Lichter, Peter, Biankin, Andrew V, Chabannon, Christian, Chin, Lynda, Clément, Bruno, de Alava, Enrique, Degos, Françoise, Ferguson, Martin L, Geary, Peter, Hayes, D Neil, Johns, Amber L, Kasprzyk, Arek, Nakagawa, Hidewaki, Penny, Robert, Piris, Miguel A, Sarin, Rajiv, Scarpa, Aldo, van de Vijver, Marc, Futreal, P Andrew, Aburatani, Hiroyuki, Bayés, Mónica, Botwell, David DL, Campbell, Peter J, Estivill, Xavier, Grimmond, Sean M, Gut, Ivo, Hirst, Martin, López-Otín, Carlos, Majumder, Partha, Marra, Marco, McPherson, John D, Ning, Zemin, Puente, Xose S, Ruan, Yijun, Stunnenberg, Hendrik G, Swerdlow, Harold, Velculescu, Victor E, Wilson, Richard K, Xue, Hong H, Yang, Liu, Spellman, Paul T, Bader, Gary D, and Boutros, Paul C

Abstract

The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

Published
2010

12. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Author

Birney, Ewan, Stamatoyannopoulos, John A., Dutta, Anindya, Guigó, Roderic, Gingeras, Thomas R., Margulies, Elliott H., Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T., Thurman, Robert E., Kuehn, Michael S., Taylor, Christopher M., Neph, Shane, Koch, Christoph M., Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A., Andrews, Robert M., Flicek, Paul, Boyle, Patrick J., Cao, Hua, Carter, Nigel P., Clelland, Gayle K., Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C., Dorschner, Michael O., Fiegler, Heike, Giresi, Paul G., Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D., Johnson, Brett E., Johnson, Ericka M., Frum, Tristan T., Rosenzweig, Elizabeth R., Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C., Navas, Patrick A., Neri, Fidencio, Parker, Stephen C., Sabo, Peter J., Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu, Man, Collins, Francis S., Dekker, Job, Lieb, Jason D., Tullius, Thomas D., Crawford, Gregory E., Sunyaev, Shamil, Noble, William S., Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L., Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A., Sekinger, Edward A., Lagarde, Julien, Abril, Josep F., Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermüller, Jörg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S., Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C., Thomas, Daryl J., Weirauch, Matthew T., Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K. G., Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L., Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G., Brown, James B., Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N., Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S., Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M., Rogers, Jane, Stadler, Peter F., Lowe, Todd M., Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E., Fu, Yutao, Green, Eric D., Karaöz, U., Siepel, Adam, Taylor, James, Liefer, Laura A, Wetterstrand, Kris A., Good, Peter J., Feingold, Elise A., Guyer, Mark S., Cooper, Gregory M., Asimenos, George, Dewey, Colin N., Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I., Löytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R., Holmes, Ian, Mullikin, James C., Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W. James, Stone, Eric A., Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C., Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D., Zhang, Zhengdong D., Barrera, Leah, Stuart, Rhona, King, David C., Ameur, Adam, Enroth, Stefan, Bieda, Mark C., Kim, Jonghwan, Bhinge, Akshay A., Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B., Lee, Charlie W., Ng, Patrick, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J., Inman, David, Singer, Michael A., Richmond, Todd A., Munn, Kyle J., Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C., Couttet, Phillippe, Bruce, Alexander W., Dovey, Oliver M., Ellis, Peter D., Langford, Cordelia F., Nix, David A., Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E., Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Kim, Tae Hoon, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K., Rosenfeld, M. Geoff, Aldred, Shelley Force, Cooper, Sara J., Halees, Anason, Lin, Jane M., Shulha, Hennady P., Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N., Yu, Yong, Iyer, Vishwanath R., Green, Roland D., Wadelius, Claes, Farnham, Peggy J., Ren, Bing, Harte, Rachel A., Hinrichs, Angie S., Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S., Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M., Karolchik, Donna, Armengol, Lluis, Bird, Christine P., de Bakker, Paul I., Kern, Andrew D., Lopez-Bigas, Nuria, Martin, Joel D., Stranger, Barbara E., Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrí­msdóttir, Ingileif B., Huppert, Julian, Zody, Michael C., Abecasis, G. R., Estivill, Xavier, Bouffard, Gerard G., Guan, Xiaobin, Hansen, Nancy F., Idol, Jacquelyn R., Maduro, Valerie V., Maskeri, Baishali, McDowell, Jennifer C., Park, Morgan, Thomas, Pamela J., Young, Alice C., Blakesley, Robert W., Muzny, Donna M., Sodergren, Erica, Wheeler, David A., Worley, Kim C., Jiang, Huaiyang, Weinstock, George M., Gibbs, Richard A., Graves, Tina, Fulton, Robert, Mardis, Elaine R., Wilson, Richard K., Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B., Chang, Jean L., Lindblad-Toh, Kerstin, Lander, Eric S., Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, de Jong, Pieter J., Birney, Ewan, Stamatoyannopoulos, John A., Dutta, Anindya, Guigó, Roderic, Gingeras, Thomas R., Margulies, Elliott H., Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T., Thurman, Robert E., Kuehn, Michael S., Taylor, Christopher M., Neph, Shane, Koch, Christoph M., Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A., Andrews, Robert M., Flicek, Paul, Boyle, Patrick J., Cao, Hua, Carter, Nigel P., Clelland, Gayle K., Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C., Dorschner, Michael O., Fiegler, Heike, Giresi, Paul G., Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D., Johnson, Brett E., Johnson, Ericka M., Frum, Tristan T., Rosenzweig, Elizabeth R., Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C., Navas, Patrick A., Neri, Fidencio, Parker, Stephen C., Sabo, Peter J., Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu, Man, Collins, Francis S., Dekker, Job, Lieb, Jason D., Tullius, Thomas D., Crawford, Gregory E., Sunyaev, Shamil, Noble, William S., Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L., Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A., Sekinger, Edward A., Lagarde, Julien, Abril, Josep F., Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermüller, Jörg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S., Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C., Thomas, Daryl J., Weirauch, Matthew T., Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K. G., Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L., Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G., Brown, James B., Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N., Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S., Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M., Rogers, Jane, Stadler, Peter F., Lowe, Todd M., Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E., Fu, Yutao, Green, Eric D., Karaöz, U., Siepel, Adam, Taylor, James, Liefer, Laura A, Wetterstrand, Kris A., Good, Peter J., Feingold, Elise A., Guyer, Mark S., Cooper, Gregory M., Asimenos, George, Dewey, Colin N., Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I., Löytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R., Holmes, Ian, Mullikin, James C., Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W. James, Stone, Eric A., Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C., Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D., Zhang, Zhengdong D., Barrera, Leah, Stuart, Rhona, King, David C., Ameur, Adam, Enroth, Stefan, Bieda, Mark C., Kim, Jonghwan, Bhinge, Akshay A., Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B., Lee, Charlie W., Ng, Patrick, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J., Inman, David, Singer, Michael A., Richmond, Todd A., Munn, Kyle J., Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C., Couttet, Phillippe, Bruce, Alexander W., Dovey, Oliver M., Ellis, Peter D., Langford, Cordelia F., Nix, David A., Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E., Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Kim, Tae Hoon, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K., Rosenfeld, M. Geoff, Aldred, Shelley Force, Cooper, Sara J., Halees, Anason, Lin, Jane M., Shulha, Hennady P., Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N., Yu, Yong, Iyer, Vishwanath R., Green, Roland D., Wadelius, Claes, Farnham, Peggy J., Ren, Bing, Harte, Rachel A., Hinrichs, Angie S., Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S., Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M., Karolchik, Donna, Armengol, Lluis, Bird, Christine P., de Bakker, Paul I., Kern, Andrew D., Lopez-Bigas, Nuria, Martin, Joel D., Stranger, Barbara E., Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrí­msdóttir, Ingileif B., Huppert, Julian, Zody, Michael C., Abecasis, G. R., Estivill, Xavier, Bouffard, Gerard G., Guan, Xiaobin, Hansen, Nancy F., Idol, Jacquelyn R., Maduro, Valerie V., Maskeri, Baishali, McDowell, Jennifer C., Park, Morgan, Thomas, Pamela J., Young, Alice C., Blakesley, Robert W., Muzny, Donna M., Sodergren, Erica, Wheeler, David A., Worley, Kim C., Jiang, Huaiyang, Weinstock, George M., Gibbs, Richard A., Graves, Tina, Fulton, Robert, Mardis, Elaine R., Wilson, Richard K., Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B., Chang, Jean L., Lindblad-Toh, Kerstin, Lander, Eric S., Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, and de Jong, Pieter J.

Abstract

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Published
2007
Full Text
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13. Mapping of transcription factor binding regions in mammalian cells by ChIP : comparison of array- and sequencing-based technologies.

Author

Euskirchen, Ghia M, Rozowsky, Joel S, Wei, Chia-Lin, Lee, Wah Heng, Zhang, Zhengdong D, Hartman, Stephen, Emanuelsson, Olof, Stolc, Viktor, Weissman, Sherman, Gerstein, Mark B, Ruan, Yijun, Snyder, Michael, Euskirchen, Ghia M, Rozowsky, Joel S, Wei, Chia-Lin, Lee, Wah Heng, Zhang, Zhengdong D, Hartman, Stephen, Emanuelsson, Olof, Stolc, Viktor, Weissman, Sherman, Gerstein, Mark B, Ruan, Yijun, and Snyder, Michael

Abstract

Recent progress in mapping transcription factor (TF) binding regions can largely be credited to chromatin immunoprecipitation (ChIP) technologies. We compared strategies for mapping TF binding regions in mammalian cells using two different ChIP schemes: ChIP with DNA microarray analysis (ChIP-chip) and ChIP with DNA sequencing (ChIP-PET). We first investigated parameters central to obtaining robust ChIP-chip data sets by analyzing STAT1 targets in the ENCODE regions of the human genome, and then compared ChIP-chip to ChIP-PET. We devised methods for scoring and comparing results among various tiling arrays and examined parameters such as DNA microarray format, oligonucleotide length, hybridization conditions, and the use of competitor Cot-1 DNA. The best performance was achieved with high-density oligonucleotide arrays, oligonucleotides >/=50 bases (b), the presence of competitor Cot-1 DNA and hybridizations conducted in microfluidics stations. When target identification was evaluated as a function of array number, 80%-86% of targets were identified with three or more arrays. Comparison of ChIP-chip with ChIP-PET revealed strong agreement for the highest ranked targets with less overlap for the low ranked targets. With advantages and disadvantages unique to each approach, we found that ChIP-chip and ChIP-PET are frequently complementary in their relative abilities to detect STAT1 targets for the lower ranked targets; each method detected validated targets that were missed by the other method. The most comprehensive list of STAT1 binding regions is obtained by merging results from ChIP-chip and ChIP-sequencing. Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies.

Published
2007
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14. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Author

Birney, Ewan, Stamatoyannopoulos, John A, Dutta, Anindya, Guigó, Roderic, Gingeras, Thomas R, Margulies, Elliott H, Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T, Thurman, Robert E, Kuehn, Michael S, Taylor, Christopher M, Neph, Shane, Koch, Christoph M, Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A, Andrews, Robert M, Flicek, Paul, Boyle, Patrick J, Cao, Hua, Carter, Nigel P, Clelland, Gayle K, Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C, Dorschner, Michael O, Fiegler, Heike, Giresi, Paul G, Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D, Johnson, Brett E, Johnson, Ericka M, Frum, Tristan T, Rosenzweig, Elizabeth R, Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C, Navas, Patrick A, Neri, Fidencio, Parker, Stephen C J, Sabo, Peter J, Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu, Man, Collins, Francis S, Dekker, Job, Lieb, Jason D, Tullius, Thomas D, Crawford, Gregory E, Sunyaev, Shamil, Noble, William S, Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L, Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A, Sekinger, Edward A, Lagarde, Julien, Abril, Josep F, Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermüller, Jörg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S, Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C, Thomas, Daryl J, Weirauch, Matthew T, Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K G, Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L, Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G, Brown, James B, Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N, Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S, Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M, Rogers, Jane, Stadler, Peter F, Lowe, Todd M, Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E, Fu, Yutao, Green, Eric D, Karaöz, Ulaş, Siepel, Adam, Taylor, James, Liefer, Laura A, Wetterstrand, Kris A, Good, Peter J, Feingold, Elise A, Guyer, Mark S, Cooper, Gregory M, Asimenos, George, Dewey, Colin N, Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I, Löytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R, Holmes, Ian, Mullikin, James C, Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W James, Stone, Eric A, Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C, Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D, Zhang, Zhengdong D, Barrera, Leah, Stuart, Rhona, King, David C, Ameur, Adam, Enroth, Stefan, Bieda, Mark C, Kim, Jonghwan, Bhinge, Akshay A, Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B, Lee, Charlie W H, Ng, Patrick, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J, Inman, David, Singer, Michael A, Richmond, Todd A, Munn, Kyle J, Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C, Couttet, Phillippe, Bruce, Alexander W, Dovey, Oliver M, Ellis, Peter D, Langford, Cordelia F, Nix, David A, Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E, Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Kim, Tae Hoon, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K, Rosenfeld, M Geoff, Aldred, Shelley Force, Cooper, Sara J, Halees, Anason, Lin, Jane M, Shulha, Hennady P, Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N S, Yu, Yong, Iyer, Vishwanath R, Green, Roland D, Wadelius, Claes, Farnham, Peggy J, Ren, Bing, Harte, Rachel A, Hinrichs, Angie S, Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S, Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M, Karolchik, Donna, Armengol, Lluis, Bird, Christine P, de Bakker, Paul I W, Kern, Andrew D, Lopez-Bigas, Nuria, Martin, Joel D, Stranger, Barbara E, Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrímsdóttir, Ingileif B, Huppert, Julian, Zody, Michael C, Abecasis, Gonçalo R, Estivill, Xavier, Bouffard, Gerard G, Guan, Xiaobin, Hansen, Nancy F, Idol, Jacquelyn R, Maduro, Valerie V B, Maskeri, Baishali, McDowell, Jennifer C, Park, Morgan, Thomas, Pamela J, Young, Alice C, Blakesley, Robert W, Muzny, Donna M, Sodergren, Erica, Wheeler, David A, Worley, Kim C, Jiang, Huaiyang, Weinstock, George M, Gibbs, Richard A, Graves, Tina, Fulton, Robert, Mardis, Elaine R, Wilson, Richard K, Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B, Chang, Jean L, Lindblad-Toh, Kerstin, Lander, Eric S, Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, de Jong, Pieter J, Birney, Ewan, Stamatoyannopoulos, John A, Dutta, Anindya, Guigó, Roderic, Gingeras, Thomas R, Margulies, Elliott H, Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T, Thurman, Robert E, Kuehn, Michael S, Taylor, Christopher M, Neph, Shane, Koch, Christoph M, Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A, Andrews, Robert M, Flicek, Paul, Boyle, Patrick J, Cao, Hua, Carter, Nigel P, Clelland, Gayle K, Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C, Dorschner, Michael O, Fiegler, Heike, Giresi, Paul G, Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D, Johnson, Brett E, Johnson, Ericka M, Frum, Tristan T, Rosenzweig, Elizabeth R, Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C, Navas, Patrick A, Neri, Fidencio, Parker, Stephen C J, Sabo, Peter J, Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu, Man, Collins, Francis S, Dekker, Job, Lieb, Jason D, Tullius, Thomas D, Crawford, Gregory E, Sunyaev, Shamil, Noble, William S, Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L, Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A, Sekinger, Edward A, Lagarde, Julien, Abril, Josep F, Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermüller, Jörg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S, Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C, Thomas, Daryl J, Weirauch, Matthew T, Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K G, Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L, Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G, Brown, James B, Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N, Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S, Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M, Rogers, Jane, Stadler, Peter F, Lowe, Todd M, Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E, Fu, Yutao, Green, Eric D, Karaöz, Ulaş, Siepel, Adam, Taylor, James, Liefer, Laura A, Wetterstrand, Kris A, Good, Peter J, Feingold, Elise A, Guyer, Mark S, Cooper, Gregory M, Asimenos, George, Dewey, Colin N, Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I, Löytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R, Holmes, Ian, Mullikin, James C, Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W James, Stone, Eric A, Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C, Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D, Zhang, Zhengdong D, Barrera, Leah, Stuart, Rhona, King, David C, Ameur, Adam, Enroth, Stefan, Bieda, Mark C, Kim, Jonghwan, Bhinge, Akshay A, Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B, Lee, Charlie W H, Ng, Patrick, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J, Inman, David, Singer, Michael A, Richmond, Todd A, Munn, Kyle J, Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C, Couttet, Phillippe, Bruce, Alexander W, Dovey, Oliver M, Ellis, Peter D, Langford, Cordelia F, Nix, David A, Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E, Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Kim, Tae Hoon, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K, Rosenfeld, M Geoff, Aldred, Shelley Force, Cooper, Sara J, Halees, Anason, Lin, Jane M, Shulha, Hennady P, Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N S, Yu, Yong, Iyer, Vishwanath R, Green, Roland D, Wadelius, Claes, Farnham, Peggy J, Ren, Bing, Harte, Rachel A, Hinrichs, Angie S, Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S, Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M, Karolchik, Donna, Armengol, Lluis, Bird, Christine P, de Bakker, Paul I W, Kern, Andrew D, Lopez-Bigas, Nuria, Martin, Joel D, Stranger, Barbara E, Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrímsdóttir, Ingileif B, Huppert, Julian, Zody, Michael C, Abecasis, Gonçalo R, Estivill, Xavier, Bouffard, Gerard G, Guan, Xiaobin, Hansen, Nancy F, Idol, Jacquelyn R, Maduro, Valerie V B, Maskeri, Baishali, McDowell, Jennifer C, Park, Morgan, Thomas, Pamela J, Young, Alice C, Blakesley, Robert W, Muzny, Donna M, Sodergren, Erica, Wheeler, David A, Worley, Kim C, Jiang, Huaiyang, Weinstock, George M, Gibbs, Richard A, Graves, Tina, Fulton, Robert, Mardis, Elaine R, Wilson, Richard K, Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B, Chang, Jean L, Lindblad-Toh, Kerstin, Lander, Eric S, Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, and de Jong, Pieter J

Abstract

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function., QC 20111222

Published
2007
Full Text
View/download PDF

15. Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies.

Author

Euskirchen, Ghia M, Rozowsky, Joel S, Wei, Chia-Lin, Lee, Wah Heng, Zhang, Zhengdong D, Hartman, Stephen, Emanuelsson, Olof, Stolc, Viktor, Weissman, Sherman, Gerstein, Mark B, Ruan, Yijun, Snyder, Michael, Euskirchen, Ghia M, Rozowsky, Joel S, Wei, Chia-Lin, Lee, Wah Heng, Zhang, Zhengdong D, Hartman, Stephen, Emanuelsson, Olof, Stolc, Viktor, Weissman, Sherman, Gerstein, Mark B, Ruan, Yijun, and Snyder, Michael

Published
2007

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