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Mapping the cellular response to small molecules using chemogenomic fitness signatures.

Bibliographic reference Lee, Anna Y ; St Onge, Robert P ; Proctor, Michael J ; Wallace, Iain M ; Nile, Aaron H ; et. al. Mapping the cellular response to small molecules using chemogenomic fitness signatures.. In: Science, Vol. 344, no. 6180, p. 208-211 (2014)
Permanent URL http://hdl.handle.net/2078.1/142744
  1. Barrett P. M., Alagely A., Topol E. J., Cystic fibrosis in an era of genomically guided therapy, 10.1093/hmg/dds345
  2. Lamb J., The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease, 10.1126/science.1132939
  3. Iorio F., Bosotti R., Scacheri E., Belcastro V., Mithbaokar P., Ferriero R., Murino L., Tagliaferri R., Brunetti-Pierri N., Isacchi A., di Bernardo D., Discovery of drug mode of action and drug repositioning from transcriptional responses, 10.1073/pnas.1000138107
  4. Giaever Guri, Chu Angela M., Ni Li, Connelly Carla, Riles Linda, Véronneau Steeve, Dow Sally, Lucau-Danila Ankuta, Anderson Keith, André Bruno, Arkin Adam P., Astromoff Anna, El Bakkoury Mohamed, Bangham Rhonda, Benito Rocio, Brachat Sophie, Campanaro Stefano, Curtiss Matt, Davis Karen, Deutschbauer Adam, Entian Karl-Dieter, Flaherty Patrick, Foury Francoise, Garfinkel David J., Gerstein Mark, Gotte Deanna, Güldener Ulrich, Hegemann Johannes H., Hempel Svenja, Herman Zelek, Jaramillo Daniel F., Kelly Diane E., Kelly Steven L., Kötter Peter, LaBonte Darlene, Lamb David C., Lan Ning, Liang Hong, Liao Hong, Liu Lucy, Luo Chuanyun, Lussier Marc, Mao Rong, Menard Patrice, Ooi Siew Loon, Revuelta Jose L., Roberts Christopher J., Rose Matthias, Ross-Macdonald Petra, Scherens Bart, Schimmack Greg, Shafer Brenda, Shoemaker Daniel D., Sookhai-Mahadeo Sharon, Storms Reginald K., Strathern Jeffrey N., Valle Giorgio, Voet Marleen, Volckaert Guido, Wang Ching-yun, Ward Teresa R., Wilhelmy Julie, Winzeler Elizabeth A., Yang Yonghong, Yen Grace, Youngman Elaine, Yu Kexin, Bussey Howard, Boeke Jef D., Snyder Michael, Philippsen Peter, Davis Ronald W., Johnston Mark, Functional profiling of the Saccharomyces cerevisiae genome, 10.1038/nature00935
  5. Giaever G., Flaherty P., Kumm J., Proctor M., Nislow C., Jaramillo D. F., Chu A. M., Jordan M. I., Arkin A. P., Davis R. W., Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast, 10.1073/pnas.0307490100
  6. Lum Pek Yee, Armour Christopher D., Stepaniants Sergey B., Cavet Guy, Wolf Maria K., Butler J.Scott, Hinshaw Jerald C., Garnier Philippe, Prestwich Glenn D., Leonardson Amy, Garrett-Engele Philip, Rush Christopher M., Bard Martin, Schimmack Greg, Phillips John W., Roberts Christopher J., Shoemaker Daniel D., Discovering Modes of Action for Therapeutic Compounds Using a Genome-Wide Screen of Yeast Heterozygotes, 10.1016/s0092-8674(03)01035-3
  7. Hillenmeyer M. E., Fung E., Wildenhain J., Pierce S. E., Hoon S., Lee W., Proctor M., St.Onge R. P., Tyers M., Koller D., Altman R. B., Davis R. W., Nislow C., Giaever G., The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes, 10.1126/science.1150021
  8. Giaever Guri, Shoemaker Daniel D., Jones Ted W., Liang Hong, Winzeler Elizabeth A., Astromoff Anna, Davis Ronald W., 10.1038/6791
  9. Parsons Ainslie B, Brost Renée L, Ding Huiming, Li Zhijian, Zhang Chaoying, Sheikh Bilal, Brown Grant W, Kane Patricia M, Hughes Timothy R, Boone Charles, Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways, 10.1038/nbt919
  10. Wallace Iain M., Urbanus Malene L., Luciani Genna M., Burns Andrew R., Han Mitchell K.L., Wang Hao, Arora Kriti, Heisler Lawrence E., Proctor Michael, St. Onge Robert P., Roemer Terry, Roy Peter J., Cummins Carolyn L., Bader Gary D., Nislow Corey, Giaever Guri, Compound Prioritization Methods Increase Rates of Chemical Probe Discovery in Model Organisms, 10.1016/j.chembiol.2011.07.018
  11. Torres Nikko P., Lee Anna Y., Giaever Guri, Nislow Corey, Brown Grant W., A High-Throughput Yeast Assay Identifies Synergistic Drug Combinations, 10.1089/adt.2012.503
  12. Hu Qicong, Nelson W. James, Spiliotis Elias T., Forchlorfenuron Alters Mammalian Septin Assembly, Organization, and Dynamics, 10.1074/jbc.m804962200
  13. 10, 76 (2014)
  14. Cleves Ann E., McGee Todd P., Whitters Eric A., Champlon Kathleen M., Altken Jacqueline R., Dowhan William, Goebl Mark, Bankaitis Vytas A., Mutations in the CDP-choline pathway for phospholipid biosynthesis bypass the requirement for an essential phospholipid transfer protein, 10.1016/0092-8674(91)90508-v
  15. The EMBO Journal, 15, 6447 (1996)
  16. Chatr-aryamontri A., Breitkreutz B.-J., Heinicke S., Boucher L., Winter A., Stark C., Nixon J., Ramage L., Kolas N., O'Donnell L., Reguly T., Breitkreutz A., Sellam A., Chen D., Chang C., Rust J., Livstone M., Oughtred R., Dolinski K., Tyers M., The BioGRID interaction database: 2013 update, 10.1093/nar/gks1158
  17. Costanzo M., Baryshnikova A., Bellay J., Kim Y., Spear E. D., Sevier C. S., Ding H., Koh J. L.Y., Toufighi K., Mostafavi S., Prinz J., St. Onge R. P., VanderSluis B., Makhnevych T., Vizeacoumar F. J., Alizadeh S., Bahr S., Brost R. L., Chen Y., Cokol M., Deshpande R., Li Z., Lin Z.-Y., Liang W., Marback M., Paw J., San Luis B.-J., Shuteriqi E., Tong A. H. Y., van Dyk N., Wallace I. M., Whitney J. A., Weirauch M. T., Zhong G., Zhu H., Houry W. A., Brudno M., Ragibizadeh S., Papp B., Pal C., Roth F. P., Giaever G., Nislow C., Troyanskaya O. G., Bussey H., Bader G. D., Gingras A.-C., Morris Q. D., Kim P. M., Kaiser C. A., Myers C. L., Andrews B. J., Boone C., The Genetic Landscape of a Cell, 10.1126/science.1180823
  18. Anderson Nora, Borlak Jürgen, Drug-induced phospholipidosis, 10.1016/j.febslet.2006.08.061
  19. Reasor, Experimental Biology and Medicine, 226, 825 (2001)
  20. Rainey M. M., Korostyshevsky D., Lee S., Perlstein E. O., The Antidepressant Sertraline Targets Intracellular Vesiculogenic Membranes in Yeast, 10.1534/genetics.110.117846
  21. Škrtić Marko, Sriskanthadevan Shrivani, Jhas Bozhena, Gebbia Marinella, Wang Xiaoming, Wang Zezhou, Hurren Rose, Jitkova Yulia, Gronda Marcela, Maclean Neil, Lai Courteney K., Eberhard Yanina, Bartoszko Justyna, Spagnuolo Paul, Rutledge Angela C., Datti Alessandro, Ketela Troy, Moffat Jason, Robinson Brian H., Cameron Jessie H., Wrana Jeffery, Eaves Connie J., Minden Mark D., Wang Jean C.Y., Dick John E., Humphries Keith, Nislow Corey, Giaever Guri, Schimmer Aaron D., Inhibition of Mitochondrial Translation as a Therapeutic Strategy for Human Acute Myeloid Leukemia, 10.1016/j.ccr.2011.10.015
  22. Blackman Ronald K., Cheung-Ong Kahlin, Gebbia Marinella, Proia David A., He Suqin, Kepros Jane, Jonneaux Aurelie, Marchetti Philippe, Kluza Jerome, Rao Patricia E., Wada Yumiko, Giaever Guri, Nislow Corey, Mitochondrial Electron Transport Is the Cellular Target of the Oncology Drug Elesclomol, 10.1371/journal.pone.0029798
  23. Hoon Shawn, M Smith Andrew, Wallace Iain M, Suresh Sundari, Miranda Molly, Fung Eula, Proctor Michael, Shokat Kevan M, Zhang Chao, Davis Ronald W, Giaever Guri, StOnge Robert P, Nislow Corey, An integrated platform of genomic assays reveals small-molecule bioactivities, 10.1038/nchembio.100
  24. Pierce Sarah E, Davis Ron W, Nislow Corey, Giaever Guri, Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures, 10.1038/nprot.2007.427
  25. Vichai Vanicha, Kirtikara Kanyawim, Sulforhodamine B colorimetric assay for cytotoxicity screening, 10.1038/nprot.2006.179
  26. Pierce Sarah E, Fung Eula L, Jaramillo Daniel F, Chu Angela M, Davis Ronald W, Nislow Corey, Giaever Guri, A unique and universal molecular barcode array, 10.1038/nmeth905
  27. Jain Shobhit, Bader Gary D, An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology, 10.1186/1471-2105-11-562
  28. Mecham Brigham H., Nelson Peter S., Storey John D., Supervised normalization of microarrays, 10.1093/bioinformatics/btq118
  29. Benschop Joris J., Brabers Nathalie, van Leenen Dik, Bakker Linda V., van Deutekom Hanneke W.M., van Berkum Nynke L., Apweiler Eva, Lijnzaad Philip, Holstege Frank C.P., Kemmeren Patrick, A Consensus of Core Protein Complex Compositions for Saccharomyces cerevisiae, 10.1016/j.molcel.2010.06.002
  30. J R STAT SOC B, 57, 289 (1995)
  31. Zambon Alexander C., Gaj Stan, Ho Isaac, Hanspers Kristina, Vranizan Karen, Evelo Chris T., Conklin Bruce R., Pico Alexander R., Salomonis Nathan, GO-Elite: a flexible solution for pathway and ontology over-representation, 10.1093/bioinformatics/bts366
  32. Merico Daniele, Isserlin Ruth, Stueker Oliver, Emili Andrew, Bader Gary D., Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation, 10.1371/journal.pone.0013984
  33. Smoot M. E., Ono K., Ruscheinski J., Wang P.-L., Ideker T., Cytoscape 2.8: new features for data integration and network visualization, 10.1093/bioinformatics/btq675
  34. WHITLOCK M. C., Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach : Combining probabilities from many tests, 10.1111/j.1420-9101.2005.00917.x
  35. Bemis Guy W., Murcko Mark A., The Properties of Known Drugs. 1. Molecular Frameworks, 10.1021/jm9602928
  36. Halliwell William H., Cationic Amphiphilic Drug-Induced Phospholipidosis, 10.1177/019262339702500111
  37. O'Boyle Noel M, Banck Michael, James Craig A, Morley Chris, Vandermeersch Tim, Hutchison Geoffrey R, Open Babel: An open chemical toolbox, 10.1186/1758-2946-3-33
  38. Langfelder Peter, Zhang Bin, Horvath Steve, Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R, 10.1093/bioinformatics/btm563
  39. Van Dongen Stijn, Graph Clustering Via a Discrete Uncoupling Process, 10.1137/040608635
  40. Bergmann Sven, Ihmels Jan, Barkai Naama, Iterative signature algorithm for the analysis of large-scale gene expression data, 10.1103/physreve.67.031902
  41. Rogers David, Brown Robert D., Hahn Mathew, Using Extended-Connectivity Fingerprints with Laplacian-Modified Bayesian Analysis in High-Throughput Screening Follow-Up, 10.1177/1087057105281365
  42. Gleeson M. Paul, Hersey Anne, Montanari Dino, Overington John, Probing the links between in vitro potency, ADMET and physicochemical parameters, 10.1038/nrd3367
  43. Goffeau André, Dufour Jean-Pierre, [39] Plasma membrane ATPase from the yeast Saccharomyces cerevisiae, Methods in Enzymology (1988) ISBN:9780121820589 p.528-533, 10.1016/0076-6879(88)57101-x
  44. Schaaf Gabriel, Ortlund Eric A., Tyeryar Kimberly R., Mousley Carl J., Ile Kristina E., Garrett Teresa A., Ren Jihui, Woolls Melissa J., Raetz Christian R.H., Redinbo Matthew R., Bankaitis Vytas A., Functional Anatomy of Phospholipid Binding and Regulation of Phosphoinositide Homeostasis by Proteins of the Sec14 Superfamily, 10.1016/j.molcel.2007.11.026
  45. Schaaf G., Dynowski M., Mousley C. J., Shah S. D., Yuan P., Winklbauer E. M., de Campos M. K. F., Trettin K., Quinones M.-C., Smirnova T. I., Yanagisawa L. L., Ortlund E. A., Bankaitis V. A., Resurrection of a functional phosphatidylinositol transfer protein from a pseudo-Sec14 scaffold by directed evolution, 10.1091/mbc.e10-11-0903
  46. Phillips Scott E, Sha Bingdong, Topalof Lora, Xie Zhigang, Alb James G, Klenchin Vadim A, Swigart Phil, Cockcroft Shamshad, Martin Thomas F.J, Luo Ming, Bankaitis Vytas A, Yeast Sec14p Deficient in Phosphatidylinositol Transfer Activity Is Functional In Vivo, 10.1016/s1097-2765(00)80366-4
  47. Li X., Routt S. M., Xie Z., Cui X., Fang M., Kearns M. A., Bard M., Kirsch D. R., Bankaitis V. A., Identification of a Novel Family of Nonclassic Yeast Phosphatidylinositol Transfer Proteins Whose Function Modulates Phospholipase D Activity and Sec14p-independent Cell Growth, 10.1091/mbc.11.6.1989
  48. Spagnuolo P. A., Hu J., Hurren R., Wang X., Gronda M., Sukhai M. A., Di Meo A., Boss J., Ashali I., Beheshti Zavareh R., Fine N., Simpson C. D., Sharmeen S., Rottapel R., Schimmer A. D., The antihelmintic flubendazole inhibits microtubule function through a mechanism distinct from Vinca alkaloids and displays preclinical activity in leukemia and myeloma, 10.1182/blood-2009-09-243055
  49. Lawo Steffen, Bashkurov Mikhail, Mullin Michael, Ferreria Mariana Gomez, Kittler Ralf, Habermann Bianca, Tagliaferro Andrea, Poser Ina, Hutchins James R.A., Hegemann Björn, Pinchev Deborah, Buchholz Frank, Peters Jan-Michael, Hyman Anthony A., Gingras Anne-Claude, Pelletier Laurence, HAUS, the 8-Subunit Human Augmin Complex, Regulates Centrosome and Spindle Integrity, 10.1016/j.cub.2009.04.033
  50. Benedetti H., Raths S., Crausaz F., Riezman H., The END3 gene encodes a protein that is required for the internalization step of endocytosis and for actin cytoskeleton organization in yeast., 10.1091/mbc.5.9.1023
  51. Janssen A. J.M., Trijbels F. J.M., Sengers R. C.A., Smeitink J. A.M., van den Heuvel L. P., Wintjes L. T.M., Stoltenborg-Hogenkamp B. J.M., Rodenburg R. J.T., Spectrophotometric Assay for Complex I of the Respiratory Chain in Tissue Samples and Cultured Fibroblasts, 10.1373/clinchem.2006.078873
  52. Birch-Machin Mark A, Shepherd Isobel M, Watmough Nicholas J, Sherratt H Stanley A, Bartlett Kim, Darley-Usmar Victor M, Milligan David W A, Welch Robert J, Aynsley-Green Albert, Turnbull Douglass M, Fatal Lactic Acidosis in Infancy with a Defect of Complex III of the Respiratory Chain, 10.1203/00006450-198905000-00025
  53. Krähenbühl Stephan, Talos Christine, Wiesmann Ulrich, Hoppel Charles L., Development and evaluation of a spectrophotometric assay for complex III in isolated mitochondria, tissues and fibroblasts from rats and humans, 10.1016/0009-8981(94)90270-4
  54. Trounce Ian A., Kim Yoon L., Jun Albert S., Wallace Douglas C., [42]Assessment of mitochondrial oxidative phosphorylation in patient muscle biopsies, lymphoblasts, and transmitochondrial cell lines, Methods in Enzymology (1996) ISBN:9780121821654 p.484-509, 10.1016/s0076-6879(96)64044-0
  55. Zheng X., Shoffner J. M., Lott M. T., Voljavec A. S., Krawiecki N. S., Winn K., Wallace B. C., Evidence in a lethal infantile mitochondrial disease for a nuclear mutation affecting respiratory complexes I and IV, 10.1212/wnl.39.9.1203
  56. Pietro, Journal of Biological Chemistry, 212, 941 (1955)
  57. Vashist Shilpa, Kim Woong, Belden William J., Spear Eric D., Barlowe Charles, Ng Davis T.W., Distinct retrieval and retention mechanisms are required for the quality control of endoplasmic reticulum protein folding, 10.1083/jcb.200106123
  58. Roberg Kevin J., Rowley Neil, Kaiser Chris A., Physiological Regulation of Membrane Protein Sorting Late in the Secretory Pathway ofSaccharomyces cerevisiae, 10.1083/jcb.137.7.1469
  59. Risinger A. L., Activity-dependent Reversible Inactivation of the General Amino Acid Permease, 10.1091/mbc.e06-06-0506
  60. Walters W.Patrick, Murcko Mark A, Prediction of ‘drug-likeness’, 10.1016/s0169-409x(02)00003-0
  61. Zhang Yong-Qiang, Gamarra Soledad, Garcia-Effron Guillermo, Park Steven, Perlin David S., Rao Rajini, Requirement for Ergosterol in V-ATPase Function Underlies Antifungal Activity of Azole Drugs, 10.1371/journal.ppat.1000939
  62. Perlin, Journal of Biological Chemistry, 263, 18118 (1988)