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23 results on '"Hirozane-Kishikawa, Tomoko"'

1. A Map of the Interactome Network of the Metazoan C. elegans

Author

Li, Siming, Armstrong, Christopher M., Bertin, Nicolas, Ge, Hui, Milstein, Stuart, Boxem, Mike, Vidalain, Pierre-Olivier, Han, Jing-Dong J., Chesneau, Alban, Hao, Tong, Goldberg, Debra S., Li, Ning, Martinez, Monica, Rual, Jean-François, Lamesch, Philippe, Xu, Lai, Tewari, Muneesh, Wong, Sharyl L., Zhang, Lan V., Berriz, Gabriel F., Jacotot, Laurent, Vaglio, Philippe, Reboul, Jérôme, Hirozane-Kishikawa, Tomoko, Li, Qianru, Gabel, Harrison W., Elewa, Ahmed, Baumgartner, Bridget, Rose, Debra J., Yu, Haiyuan, Bosak, Stephanie, Sequerra, Reynaldo, Fraser, Andrew, Mango, Susan E., Saxton, William M., Strome, Susan, van den Heuvel, Sander, Piano, Fabio, Vandenhaute, Jean, Sardet, Claude, Gerstein, Mark, Doucette-Stamm, Lynn, Gunsalus, Kristin C., Harper, J. Wade, Cusick, Michael E., Roth, Frederick P., Hill, David E., and Vidal, Marc

Published
2004

2. High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

Author

Yu, Haiyuan, Braun, Pascal, Yildirim, Muhammed A., Lemmens, Irma, Venkatesan, Kavitha, Sahalie, Julie, Hirozane-Kishikawa, Tomoko, Gebreab, Fana, Li, Na, Simonis, Nicolas, Hao, Tong, Rual, Jean-François, Dricot, Amélie, Vazquez, Alexei, Murray, Ryan R., Simon, Christophe, Tardivo, Leah, Tam, Stanley, Svrzikapa, Nenad, Fan, Changyu, de Smet, Anne-Sophie, Motyl, Adriana, Hudson, Michael E., Park, Juyong, Xin, Xiaofeng, Cusick, Michael E., Moore, Troy, Boone, Charlie, Snyder, Michael, Roth, Frederick P., Barabási, Albert-László, Tavernier, Jan, Hill, David E., and Vidal, Marc

Published
2008
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4. A Molecular Neuroethological Approach for Identifying and Characterizing a Cascade of Behaviorally Regulated Genes

Author

Wada, Kazuhiro, Howard, Jason T., McConnell, Patrick, Whitney, Osceola, Lints, Thierry, Rivas, Miriam V., Horita, Haruhito, Patterson, Michael A., White, Stephanie A., Scharff, Constance, Haesler, Sebastian, Zhao, Shengli, Sakaguchi, Hironobu, Hagiwara, Masatoshi, Shiraki, Toshiyuki, Hirozane-Kishikawa, Tomoko, Skene, Pate, Hayashizaki, Yoshihide, Carninci, Piero, and Jarvis, Erich D.

Published
2006
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5. Towards a proteome-scale map of the human protein-protein interaction network

Author

Rual, Jean-François, Venkatesan, Kavitha, Hao, Tong, Hirozane-Kishikawa, Tomoko, Dricot, Amélie, Li, Ning, Berriz, Gabriel F., Gibbons, Francis D., Dreze, Matija, Ayivi-Guedehoussou, Nono, Klitgord, Niels, Simon, Christophe, Boxem, Mike, Milstein, Stuart, Rosenberg, Jennifer, Goldberg, Debra S., Zhang, Lan V., Wong, Sharyl L., Franklin, Giovanni, Li, Siming, Albala, Joanna S., Lim, Janghoo, Fraughton, Carlene, Llamosas, Estelle, Cevik, Sebiha, Bex, Camille, Lamesch, Philippe, Sikorski, Robert S., Vandenhaute, Jean, Zoghbi, Huda Y., Smolyar, Alex, Bosak, Stephanie, Sequerra, Reynaldo, Doucette-Stamm, Lynn, Cusick, Michael E., Hill, David E., Roth, Frederick P., and Vidal, Marc

Published
2005

6. Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses

Author

Simonis Nicolas, Rual Jean-François, Lemmens Irma, Boxus Mathieu, Hirozane-Kishikawa Tomoko, Gatot Jean-Stéphane, Dricot Amélie, Hao Tong, Vertommen Didier, Legros Sébastien, Daakour Sarah, Klitgord Niels, Martin Maud, Willaert Jean-François, Dequiedt Franck, Navratil Vincent, Cusick Michael E, Burny Arsène, Van Lint Carine, Hill David E, Tavernier Jan, Kettmann Richard, Vidal Marc, and Twizere Jean-Claude

Subjects
HTLV, Interactome, Retrovirus, ORFeome, Tax, HBZ, Immunologic diseases. Allergy, RC581-607
Abstract

Abstract Background Human T-cell leukemia virus type 1 (HTLV-1) and type 2 both target T lymphocytes, yet induce radically different phenotypic outcomes. HTLV-1 is a causative agent of Adult T-cell leukemia (ATL), whereas HTLV-2, highly similar to HTLV-1, causes no known overt disease. HTLV gene products are engaged in a dynamic struggle of activating and antagonistic interactions with host cells. Investigations focused on one or a few genes have identified several human factors interacting with HTLV viral proteins. Most of the available interaction data concern the highly investigated HTLV-1 Tax protein. Identifying shared and distinct host-pathogen protein interaction profiles for these two viruses would enlighten how they exploit distinctive or common strategies to subvert cellular pathways toward disease progression. Results We employ a scalable methodology for the systematic mapping and comparison of pathogen-host protein interactions that includes stringent yeast two-hybrid screening and systematic retest, as well as two independent validations through an additional protein interaction detection method and a functional transactivation assay. The final data set contained 166 interactions between 10 viral proteins and 122 human proteins. Among the 166 interactions identified, 87 and 79 involved HTLV-1 and HTLV-2 -encoded proteins, respectively. Targets for HTLV-1 and HTLV-2 proteins implicate a diverse set of cellular processes including the ubiquitin-proteasome system, the apoptosis, different cancer pathways and the Notch signaling pathway. Conclusions This study constitutes a first pass, with homogeneous data, at comparative analysis of host targets for HTLV-1 and -2 retroviruses, complements currently existing data for formulation of systems biology models of retroviral induced diseases and presents new insights on biological pathways involved in retroviral infection.

Published
2012
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8. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia

Author

Carninci, Piero, Waki, Kazunori, Shiraki, Toshiyuki, Shibata, Kazuhiro, Itoh, Masayoshi, Aizawa, Katsunori, Arakawa, Takahiro, Ishii, Yoshiyuki, Sasaki, Daisuke, Bono, Hidemasa, Kondo, Shinji, Sugahara, Yuichi, Saito, Rintaro, Osato, Naoki, Fukuda, Shiro, Sato, Kenjiro, Watahiki, Akira, Hirozane-Kishikawa, Tomoko, Nakamura, Mari, Shibata, Yuko, Yasunishi, Ayako, Kikuchi, Noriko, Yoshiki, Atsushi, Kusakabe, Moriaki, Gustincich, Stefano, Beisel, Kirk, Pavan, William, Aidinis, Vassilis, Nakagawara, Akira, Held, William A., Iwata, Hiroo, Kono, Tomohiro, Nakauchi, Hiromitsu, Lyons, Paul, Wells, Christine, Hume, David A., Fagiolini, Michela, Hensch, Takao K., Brinkmeier, Michelle, Camper, Sally, Hirota, Junji, Mombaerts, Peter, Muramatsu, Masami, Okazaki, Yasushi, Kawai, Jun, Hayashizaki, Yoshihide, and Konno, Hideaki

Subjects
Genetic research -- Analysis, Genomes -- Research, DNA -- Genetic aspects, Genetic transcription -- Physiological aspects, Health
Abstract

The authors describe the development of mouth full-length cDNA encyclopedia. They report that this encyclopedia has been constructed on the basis of preparing and sequencing cDNA libraries.

Published
2003

9. Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses.

Author

Simonis, Nicolas, Rual, Jean-François, Lemmens, Irma, Boxus, Mathieu, Hirozane-Kishikawa, Tomoko, Gatot, Jean-Stéphane, Dricot, Amélie, Hao, Tong, Vertommen, Didier, Legros, Sébastien, Daakour, Sarah, Klitgord, Niels, Martin, Maud, Willaert, Jean-François, Dequiedt, Franck, Navratil, Vincent, Cusick, Michael E, Burny, Arsène, Van Lint, Carine, Hill, David E, Tavernier, Jan, Kettmann, Richard, Vidal, Marc, Twizere, Jean-Claude, Simonis, Nicolas, Rual, Jean-François, Lemmens, Irma, Boxus, Mathieu, Hirozane-Kishikawa, Tomoko, Gatot, Jean-Stéphane, Dricot, Amélie, Hao, Tong, Vertommen, Didier, Legros, Sébastien, Daakour, Sarah, Klitgord, Niels, Martin, Maud, Willaert, Jean-François, Dequiedt, Franck, Navratil, Vincent, Cusick, Michael E, Burny, Arsène, Van Lint, Carine, Hill, David E, Tavernier, Jan, Kettmann, Richard, Vidal, Marc, and Twizere, Jean-Claude

Abstract

Human T-cell leukemia virus type 1 (HTLV-1) and type 2 both target T lymphocytes, yet induce radically different phenotypic outcomes. HTLV-1 is a causative agent of Adult T-cell leukemia (ATL), whereas HTLV-2, highly similar to HTLV-1, causes no known overt disease. HTLV gene products are engaged in a dynamic struggle of activating and antagonistic interactions with host cells. Investigations focused on one or a few genes have identified several human factors interacting with HTLV viral proteins. Most of the available interaction data concern the highly investigated HTLV-1 Tax protein. Identifying shared and distinct host-pathogen protein interaction profiles for these two viruses would enlighten how they exploit distinctive or common strategies to subvert cellular pathways toward disease progression., Comparative Study, Journal Article, Research Support, N.I.H. Extramural, Research Support, Non-U.S. Gov't, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2012

10. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

Author

Simonis, Nicolas, Rual, Jean-François, Carvunis, Anne-Ruxandra, Tasan, Murat, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, Hao, Tong, Sahalie, Julie M, Venkatesan, Kavitha, Gebreab, Fana, Cevik, Sebiha, Klitgord, Niels, Fan, Changyu, Braun, Pascal, Li, Ning, Ayivi-Guedehoussou, Nono, Dann, Elizabeth, Bertin, Nicolas, Szeto, David, Dricot, Amélie, Yildirim, Muhammed A, Lin, Chenwei, de Smet, Anne-Sophie, Kao, Huey-Ling, Simon, Christophe, Smolyar, Alex, Ahn, Jin Sook, Tewari, Muneesh, Boxem, Mike, Milstein, Stuart, Yu, Haiyuan, Dreze, Matija, Vandenhaute, Jean, Gunsalus, Kristin C, Cusick, Michael E, Hill, David E, Tavernier, Jan, Roth, Frederick P, Vidal, Marc, Simonis, Nicolas, Rual, Jean-François, Carvunis, Anne-Ruxandra, Tasan, Murat, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, Hao, Tong, Sahalie, Julie M, Venkatesan, Kavitha, Gebreab, Fana, Cevik, Sebiha, Klitgord, Niels, Fan, Changyu, Braun, Pascal, Li, Ning, Ayivi-Guedehoussou, Nono, Dann, Elizabeth, Bertin, Nicolas, Szeto, David, Dricot, Amélie, Yildirim, Muhammed A, Lin, Chenwei, de Smet, Anne-Sophie, Kao, Huey-Ling, Simon, Christophe, Smolyar, Alex, Ahn, Jin Sook, Tewari, Muneesh, Boxem, Mike, Milstein, Stuart, Yu, Haiyuan, Dreze, Matija, Vandenhaute, Jean, Gunsalus, Kristin C, Cusick, Michael E, Hill, David E, Tavernier, Jan, Roth, Frederick P, and Vidal, Marc

Abstract

To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must meet high quality standards.We present an expanded C. elegans protein-protein interaction network, or 'interactome' map, derived from testing a matrix of approximately 10,000 x approximately 10,000 proteins using a highly specific, high-throughput yeast two-hybrid system. Through a new empirical quality control framework, we show that the resulting data set (Worm Interactome 2007, or WI-2007) was similar in quality to low-throughput data curated from the literature. We filtered previous interaction data sets and integrated them with WI-2007 to generate a high-confidence consolidated map (Worm Interactome version 8, or WI8). This work allowed us to estimate the size of the worm interactome at approximately 116,000 interactions. Comparison with other types of functional genomic data shows the complementarity of distinct experimental approaches in predicting different functional relationships between genes or proteins, Journal Article, Research Support, N.I.H. Extramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S., info:eu-repo/semantics/published

Published
2009

11. An empirical framework for binary interactome mapping.

Author

Venkatesan, Kavitha, Rual, Jean-François, Vazquez, Alexei, Stelzl, Ulrich, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, Hao, Tong, Zenkner, Martina, Xin, Xiaofeng, Goh, Kwang-Il, Yildirim, Muhammed A, Simonis, Nicolas, Heinzmann, Kathrin, Gebreab, Fana, Sahalie, Julie M, Cevik, Sebiha, Simon, Christophe, de Smet, Anne-Sophie, Dann, Elizabeth, Smolyar, Alex, Vinayagam, Arunachalam, Yu, Haiyuan, Szeto, David, Borick, Heather, Dricot, Amélie, Klitgord, Niels, Murray, Ryan R, Lin, Chenwei, Lalowski, Maciej, Timm, Jan, Rau, Kirstin, Boone, Charles, Braun, Pascal, Cusick, Michael E, Roth, Frederick P, Hill, David E, Tavernier, Jan, Wanker, Erich E, Barabási, Albert-László, Vidal, Marc, Venkatesan, Kavitha, Rual, Jean-François, Vazquez, Alexei, Stelzl, Ulrich, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, Hao, Tong, Zenkner, Martina, Xin, Xiaofeng, Goh, Kwang-Il, Yildirim, Muhammed A, Simonis, Nicolas, Heinzmann, Kathrin, Gebreab, Fana, Sahalie, Julie M, Cevik, Sebiha, Simon, Christophe, de Smet, Anne-Sophie, Dann, Elizabeth, Smolyar, Alex, Vinayagam, Arunachalam, Yu, Haiyuan, Szeto, David, Borick, Heather, Dricot, Amélie, Klitgord, Niels, Murray, Ryan R, Lin, Chenwei, Lalowski, Maciej, Timm, Jan, Rau, Kirstin, Boone, Charles, Braun, Pascal, Cusick, Michael E, Roth, Frederick P, Hill, David E, Tavernier, Jan, Wanker, Erich E, Barabási, Albert-László, and Vidal, Marc

Abstract

Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets. Here we describe a framework that uses an empirically-based approach to rigorously dissect quality parameters of currently available human interactome maps. Our results indicate that high-throughput yeast two-hybrid (HT-Y2H) interactions for human proteins are more precise than literature-curated interactions supported by a single publication, suggesting that HT-Y2H is suitable to map a significant portion of the human interactome. We estimate that the human interactome contains approximately 130,000 binary interactions, most of which remain to be mapped. Similar to estimates of DNA sequence data quality and genome size early in the Human Genome Project, estimates of protein interaction data quality and interactome size are crucial to establish the magnitude of the task of comprehensive human interactome mapping and to elucidate a path toward this goal., Journal Article, Research Support, N.I.H. Extramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S., info:eu-repo/semantics/published

Published
2009

12. Next-generation sequencing to generate interactome datasets

Author

Yu, Haiyuan, primary, Tardivo, Leah, additional, Tam, Stanley, additional, Weiner, Evan, additional, Gebreab, Fana, additional, Fan, Changyu, additional, Svrzikapa, Nenad, additional, Hirozane-Kishikawa, Tomoko, additional, Rietman, Edward, additional, Yang, Xinping, additional, Sahalie, Julie, additional, Salehi-Ashtiani, Kourosh, additional, Hao, Tong, additional, Cusick, Michael E, additional, Hill, David E, additional, Roth, Frederick P, additional, Braun, Pascal, additional, and Vidal, Marc, additional

Published
2011
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14. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

Author

Simonis, Nicolas, primary, Rual, Jean-François, additional, Carvunis, Anne-Ruxandra, additional, Tasan, Murat, additional, Lemmens, Irma, additional, Hirozane-Kishikawa, Tomoko, additional, Hao, Tong, additional, Sahalie, Julie M, additional, Venkatesan, Kavitha, additional, Gebreab, Fana, additional, Cevik, Sebiha, additional, Klitgord, Niels, additional, Fan, Changyu, additional, Braun, Pascal, additional, Li, Ning, additional, Ayivi-Guedehoussou, Nono, additional, Dann, Elizabeth, additional, Bertin, Nicolas, additional, Szeto, David, additional, Dricot, Amélie, additional, Yildirim, Muhammed A, additional, Lin, Chenwei, additional, de Smet, Anne-Sophie, additional, Kao, Huey-Ling, additional, Simon, Christophe, additional, Smolyar, Alex, additional, Ahn, Jin Sook, additional, Tewari, Muneesh, additional, Boxem, Mike, additional, Milstein, Stuart, additional, Yu, Haiyuan, additional, Dreze, Matija, additional, Vandenhaute, Jean, additional, Gunsalus, Kristin C, additional, Cusick, Michael E, additional, Hill, David E, additional, Tavernier, Jan, additional, Roth, Frederick P, additional, and Vidal, Marc, additional

Published
2008
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15. An empirical framework for binary interactome mapping

Author

Venkatesan, Kavitha, primary, Rual, Jean-François, additional, Vazquez, Alexei, additional, Stelzl, Ulrich, additional, Lemmens, Irma, additional, Hirozane-Kishikawa, Tomoko, additional, Hao, Tong, additional, Zenkner, Martina, additional, Xin, Xiaofeng, additional, Goh, Kwang-Il, additional, Yildirim, Muhammed A, additional, Simonis, Nicolas, additional, Heinzmann, Kathrin, additional, Gebreab, Fana, additional, Sahalie, Julie M, additional, Cevik, Sebiha, additional, Simon, Christophe, additional, de Smet, Anne-Sophie, additional, Dann, Elizabeth, additional, Smolyar, Alex, additional, Vinayagam, Arunachalam, additional, Yu, Haiyuan, additional, Szeto, David, additional, Borick, Heather, additional, Dricot, Amélie, additional, Klitgord, Niels, additional, Murray, Ryan R, additional, Lin, Chenwei, additional, Lalowski, Maciej, additional, Timm, Jan, additional, Rau, Kirstin, additional, Boone, Charles, additional, Braun, Pascal, additional, Cusick, Michael E, additional, Roth, Frederick P, additional, Hill, David E, additional, Tavernier, Jan, additional, Wanker, Erich E, additional, Barabási, Albert-László, additional, and Vidal, Marc, additional

Published
2008
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16. Gene Organization in Rice Revealed by Full-Length cDNA Mapping and Gene Expression Analysis through Microarray

Author

Satoh, Kouji, primary, Doi, Koji, additional, Nagata, Toshifumi, additional, Kishimoto, Naoki, additional, Suzuki, Kohji, additional, Otomo, Yasuhiro, additional, Kawai, Jun, additional, Nakamura, Mari, additional, Hirozane-Kishikawa, Tomoko, additional, Kanagawa, Saeko, additional, Arakawa, Takahiro, additional, Takahashi-Iida, Juri, additional, Murata, Mitsuyoshi, additional, Ninomiya, Noriko, additional, Sasaki, Daisuke, additional, Fukuda, Shiro, additional, Tagami, Michihira, additional, Yamagata, Harumi, additional, Kurita, Kanako, additional, Kamiya, Kozue, additional, Yamamoto, Mayu, additional, Kikuta, Ari, additional, Bito, Takahito, additional, Fujitsuka, Nahoko, additional, Ito, Kazue, additional, Kanamori, Hiroyuki, additional, Choi, Il-Ryong, additional, Nagamura, Yoshiaki, additional, Matsumoto, Takashi, additional, Murakami, Kazuo, additional, Matsubara, Ken-ichi, additional, Carninci, Piero, additional, Hayashizaki, Yoshihide, additional, and Kikuchi, Shoshi, additional

Published
2007
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17. Integrative Genomic Approaches Identify IKBKE as a Breast Cancer Oncogene

Author

Boehm, Jesse S., primary, Zhao, Jean J., additional, Yao, Jun, additional, Kim, So Young, additional, Firestein, Ron, additional, Dunn, Ian F., additional, Sjostrom, Sarah K., additional, Garraway, Levi A., additional, Weremowicz, Stanislawa, additional, Richardson, Andrea L., additional, Greulich, Heidi, additional, Stewart, Carly J., additional, Mulvey, Laura A., additional, Shen, Rhine R., additional, Ambrogio, Lauren, additional, Hirozane-Kishikawa, Tomoko, additional, Hill, David E., additional, Vidal, Marc, additional, Meyerson, Matthew, additional, Grenier, Jennifer K., additional, Hinkle, Greg, additional, Root, David E., additional, Roberts, Thomas M., additional, Lander, Eric S., additional, Polyak, Kornelia, additional, and Hahn, William C., additional

Published
2007
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19. Human ORFeome Version 1.1: A Platform for Reverse Proteomics

Author

Rual, Jean-François, primary, Hirozane-Kishikawa, Tomoko, additional, Hao, Tong, additional, Bertin, Nicolas, additional, Li, Siming, additional, Dricot, Amélie, additional, Li, Ning, additional, Rosenberg, Jennifer, additional, Lamesch, Philippe, additional, Vidalain, Pierre-Olivier, additional, Clingingsmith, Tracey R., additional, Hartley, James L., additional, Esposito, Dominic, additional, Cheo, David, additional, Moore, Troy, additional, Simmons, Blake, additional, Sequerra, Reynaldo, additional, Bosak, Stephanie, additional, Doucette-Stamm, Lynn, additional, Le Peuch, Christian, additional, Vandenhaute, Jean, additional, Cusick, Michael E., additional, Albala, Joanna S., additional, Hill, David E., additional, and Vidal, Marc, additional

Published
2004
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21. A Map of the Interactome Network of the Metazoan C.elegans.

Author

Hao, Tong, Goldberg, Debra S., Li, Ning, Martinez, Monica, Ruai, Jean-François, Lamesch, Philippe, Xu, Lai, Tewari, Muneesh, Wong, Sharyl L., Zhang, Lan V., Berriz, Gabriel F., Jacotot, Laurent, Vaglio, Philippe, Reboul, Jérôme, Hirozane-Kishikawa, Tomoko, Li, Qianru, Gabel, Harrison W., Elewa, Ahmed, Baumgartner, Bridget, and Rose, Debra J.

Subjects
*CAENORHABDITIS elegans, *PROTEIN-protein interactions, *METAZOA, *PROMOTERS (Genetics), *YEAST, *DROSOPHILA
Abstract

To initiate studies on how protein-protein interaction (or "interactome") networks relate to multicellular functions, we have mapped a large fraction of the Caenorhabditis elegans interactome network. Starting with a subset of metazoan-specific proteins, more than 4000 interactions were identified from high-throughput, yeast two-hybrid (HT=Y2H) screens. Independent coaffinity purification assays experimentally validated the overall quality of this Y2H data set. Together with already described Y2H interactions and interologs predicted in sitico, the current version of the Worm Interactome (WI5) map contains ∼5500 interactions. Topological and biological features of this interactome network, as well as its integration with phenome and transcriptome data sets, lead to numerous biological hypotheses. [ABSTRACT FROM AUTHOR]

Published
2004

22. An empirical framework for binary interactome mapping.

Author

Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh KI, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, Cevik S, Simon C, de Smet AS, Dann E, Smolyar A, Vinayagam A, Yu H, Szeto D, Borick H, Dricot A, Klitgord N, Murray RR, Lin C, Lalowski M, Timm J, Rau K, Boone C, Braun P, Cusick ME, Roth FP, Hill DE, Tavernier J, Wanker EE, Barabási AL, and Vidal M

Subjects
Databases, Protein, Humans, Protein Binding, Proteins genetics, Sensitivity and Specificity, Protein Interaction Mapping methods, Proteins analysis, Proteins metabolism
Abstract

Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets. Here we describe a framework that uses an empirically-based approach to rigorously dissect quality parameters of currently available human interactome maps. Our results indicate that high-throughput yeast two-hybrid (HT-Y2H) interactions for human proteins are more precise than literature-curated interactions supported by a single publication, suggesting that HT-Y2H is suitable to map a significant portion of the human interactome. We estimate that the human interactome contains approximately 130,000 binary interactions, most of which remain to be mapped. Similar to estimates of DNA sequence data quality and genome size early in the Human Genome Project, estimates of protein interaction data quality and interactome size are crucial to establish the magnitude of the task of comprehensive human interactome mapping and to elucidate a path toward this goal.

Published
2009
Full Text
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23. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

Author

Simonis N, Rual JF, Carvunis AR, Tasan M, Lemmens I, Hirozane-Kishikawa T, Hao T, Sahalie JM, Venkatesan K, Gebreab F, Cevik S, Klitgord N, Fan C, Braun P, Li N, Ayivi-Guedehoussou N, Dann E, Bertin N, Szeto D, Dricot A, Yildirim MA, Lin C, de Smet AS, Kao HL, Simon C, Smolyar A, Ahn JS, Tewari M, Boxem M, Milstein S, Yu H, Dreze M, Vandenhaute J, Gunsalus KC, Cusick ME, Hill DE, Tavernier J, Roth FP, and Vidal M

Subjects
Animals, Caenorhabditis elegans genetics, Caenorhabditis elegans Proteins genetics, Cell Line, Humans, Protein Binding, Software, Caenorhabditis elegans metabolism, Caenorhabditis elegans Proteins analysis, Caenorhabditis elegans Proteins metabolism, Protein Interaction Mapping methods
Abstract

To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must meet high quality standards.We present an expanded C. elegans protein-protein interaction network, or 'interactome' map, derived from testing a matrix of approximately 10,000 x approximately 10,000 proteins using a highly specific, high-throughput yeast two-hybrid system. Through a new empirical quality control framework, we show that the resulting data set (Worm Interactome 2007, or WI-2007) was similar in quality to low-throughput data curated from the literature. We filtered previous interaction data sets and integrated them with WI-2007 to generate a high-confidence consolidated map (Worm Interactome version 8, or WI8). This work allowed us to estimate the size of the worm interactome at approximately 116,000 interactions. Comparison with other types of functional genomic data shows the complementarity of distinct experimental approaches in predicting different functional relationships between genes or proteins

Published
2009
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