A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles

Autor: Courtney Toder, Jodi E. Hirschman, Oana M. Enache, Larson Hogstrom, Kristin Ardlie, Ian Smith, David E. Root, Sarah A. Johnson, David L. Lahr, Bina Julian, David Wadden, Jesse S. Boehm, Nathanael S. Gray, Mariya Khan, John G. Doench, Nicholas J. Lyons, David Y. Takeda, John F. Davis, Mukta Bagul, Melanie Donahue, David Peck, Aravind Subramanian, Anita Vrcic, Desiree Davison, Steven M. Corsello, Xiaoyun Wu, Alice H. Berger, Wen-Ning Zhao, Bang Wong, Lucienne Ronco, Serena J. Silver, Willis Read-Button, Marek Orzechowski, Rajiv Narayan, Ted Natoli, Federica Piccioni, Stephen J. Haggarty, Zihan Liu, Stuart L. Schreiber, Jacqueline Rosains, Jacob K. Asiedu, Angela N. Brooks, Xiaodong Lu, Daniel D. Lam, Arthur Liberzon, Peyton Greenside, Corey Flynn, Joshua Gould, Justin Lamb, Alykhan F. Shamji, Xiaohua Wu, Joshua A. Bittker, Roger Hu, Andrew A. Tubelli, Todd R. Golub, Paul A. Clemons

Publikováno v: Cell, vol 171, iss 6

We previously piloted the concept of a Connectivity Map (CMap), whereby genes, drugs, and disease states are connected by virtue of common gene-expression signatures. Here, we report more than a 1,000-fold scale-up of the CMap as part of the NIH LINC

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6616b8e68f5b6f4bc7fabd6e75518b76
https://pubmed.ncbi.nlm.nih.gov/29195078

An extended set of yeast-based functional assays accurately identifies human disease mutations

Autor: Marc Vidal, Frederick P. Roth, Song Yi, Kara Dolinski, Charles Boone, Michael Costanzo, Tanya Tyagi, Analyn Yu, Song Sun, Rose Oughtred, Pritpal Bansal, Chandra L. Theesfeld, Cathy Tie, Nidhi Sahni, Brenda J. Andrews, Guihong Tan, David E. Hill, Jodi E. Hirschman, Fan Yang

We can now routinely identify coding variants within individual human genomes. A pressing challenge is to determine which variants disrupt the function of disease-associated genes. Both experimental and computational methods exist to predict pathogen

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b285f18e268a2c5878a14811ba3cda86
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-297290

The Gene Ontology: enhancements for 2011

Autor: P D'Eustachio, Benjamin C. Hitz, Julie Park, Paul Browne, Douglas G. Howe, Cynthia J. Krieger, Kalpana Karra, Stan Laulederkind, Karen R. Christie, Susan Tweedie, Eurie L. Hong, Lydie Bougueleret, Michele Magrane, Cathy R. Gresham, Rolf Apweiler, Lisa Matthews, Dong Li, Philippa J. Talmud, Ioannis Xenarios, J. M. Cherry, Tanya Z. Berardini, Deborah A. Siegele, Rama Balakrishnan, D. Sitnikov, A. Auchinchloss, Selina S. Dwight, Tony Sawford, Paul J. Kersey, Ruth C. Lovering, Ruth Y. Eberhardt, Ursula Hinz, Lakshmi Pillai, Sylvain Poux, Edith D. Wong, Klemens Pichler, Kati Laiho, Malcolm J. Gardner, Stephen G. Oliver, Lionel Breuza, Kara Dolinski, P Lemercier, Kristian B. Axelsen, Midori A. Harris, Adrienne E. Zweifel, H. Drabkin, Guillaume Keller, Marek S. Skrzypek, Daniel M. Staines, Fiona M. McCarthy, Nicholas H. Brown, Mark D. McDowall, Antonia Lock, Mary Shimoyama, Maria C. Costanzo, Teresia Buza, S. Jimenez, Rex L. Chisholm, Paul W. Sternberg, Hui Wang, Nadine Gruaz-Gumowski, Chantal Hulo, Rebecca E. Foulger, Melinda R. Dwinell, Judith A. Blake, Marcus C. Chibucos, B. K. McIntosh, C. D. Amundsen, Jane Lomax, L Famiglietti, Tom Hayman, Michael Tognolli, Eva Huala, James C. Hu, Patrick Masson, Maria Jesus Martin, Benoit Bely, Shuai Weng, Heather C. Wick, E. Dimmer, L. Ni, Catherine Rivoire, Christopher J. Mungall, H. Sehra, P. Duek-Roggli, Maria Victoria Schneider, Dianna G. Fisk, Michael S. Livstone, Ivo Pedruzzi, Shyamala Sundaram, Donna K. Slonim, Isabelle Cusin, Stuart R. Miyasato, Timothy F. Lowry, Varsha K. Khodiyar, Seth Carbon, Elisabeth Coudert, Jürg Bähler, Juancarlos Chan, Evelyn Camon, Daniel P. Renfro, Anne Estreicher, M. C. Blatter, Robert S. Nash, P Gaudet, Sven Heinicke, K. Van Auken, Stacia R. Engel, Alan Bridge, Ralf Stephan, Mary E. Dolan, Shane C. Burgess, Petra Fey, Shur-Jen Wang, Damien Lieberherr, Duncan Legge, P. Porras Millán, Andre Stutz, Yasmin Alam-Faruque, Gail Binkley, Bernd Roechert, S. Branconi-Quintaje, Ghislaine Argoud-Puy, S. Basu, Kim Rutherford, M. Moinat, Monte Westerfield, Arnaud Gos, Eleanor J Stanley, Valerie Wood, Ranjana Kishore, Diego Poggioli, S. Ferro-Rojas, Victoria Petri, Florence Jungo, Suzanna E. Lewis, Emmanuel Boutet, Warren A. Kibbe, M Feuermann, Claire O'Donovan, W. M. Chan, J. James, David P. Hill, Rachael P. Huntley, M. Gwinn Giglio, Paul Thomas, Jodi E. Hirschman, Paola Roncaglia

Publikováno v: Nucleic Acids Research
Nucleic Acids Research, vol. 40, no. Database issue, pp. D559-D564

The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5585f546fdf0ce700258904074512169
https://doi.org/10.1093/nar/gkr1028

The Gene Ontology project in 2008

Autor: John Day Richter, Rex L. Chisholm, Carol J. Bult, Petra Fey, Michael S. Livstone, Susan Bromberg, Evelyn Camon, Suzanna E. Lewis, Janan T. Eppig, Emily Dimmer, Mary Shimoyama, Ni Li, Rose Oughtred, Rolf Apweiler, Stuart R. Miyasato, Edith D. Wong, Tanya Z. Berardini, Maria C. Costanzo, Christopher J. Mungall, David P. Hill, Ruth C. Lovering, Valerie Wood, Marek S. Skrzypek, Jodi E. Hirschman, J. Michael Cherry, Li Donghui, Seth Carbon, Jennifer R. Wortman, Kara Dolinski, Giorgio Valle, Kathy K. Zhu, Susan Tweedie, Shane C. Burgess, Stacia R. Engel, Trudy Torto Alalibo, Paul W. Sternberg, Fiona M. McCarthy, Pankaj Jaiswal, Doug Howe, Ranjana Kishore, Jennifer I. Deegan, Warren A. Kibbe, Gail Binkley, Simon N. Twigger, Harold J. Drabkin, Erika Feltrin, Martin Aslett, Qing Dong, Matthew Berriman, David Botstein, Victoria Petri, Pascale Gaudet, Candace Collmer, Shuai Weng, Cynthia J. Krieger, Linda Hannick, Dianna G. Fisk, Robert S. Nash, Rachael P. Huntley, Nicola Mulder, Jennifer L. Smith, Sue Povey, Seung Y. Rhee, Stan Laulederkind, Benjamin C. Hitz, Julie Park, Howard J. Jacob, Midori A. Harris, Michelle G. Giglio, Judith A. Blake, Martin Ringwald, Erich M. Schwarz, Daniel Barrell, Rama Balakrishnan, Alexander D. Diehl, Trent E. Seigfried, Amelia Ireland, Eurie L. Hong, Jane Lomax, Karen Eilbeck, Michael Ashburner, Karen R. Christie, Kimberly Van Auken, Mary E. Dolan, Varsha K. Khodiyar, Monte Westerfield

Publikováno v: Nucleic Acids Research

The Gene Ontology (GO) project (http://www.geneontology.org/) provides a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://www.sequenceontology.org/). The ontologies have be

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::503d77bd60772478dfce8ffdccd16763
http://europepmc.org/articles/PMC2238979

The BioGRID interaction database: 2015 update

Autor: Rose Oughtred, Daici Chen, Lindsay Ramage, Sven Heinicke, Bobby-Joe Breitkreutz, Jennifer M. Rust, Nadine Kolas, Andrew G. Winter, Jodi E. Hirschman, Teresa Reguly, Julie Nixon, Ashton Breitkreutz, Christie S. Chang, Kara Dolinski, Mike Tyers, Chandra L. Theesfeld, Lorrie Boucher, Adnane Sellam, Lara O'Donnell, Michael S. Livstone, Andrew Chatr-aryamontri, Chris Stark

Publikováno v: Nucleic Acids Research

The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein interactions curated from the primary biomedical literature for all major model organism species an

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::279ab549976e8805da58dcf22ad52f07