Analyzing the Structure, Function and Information Flow in Signaling Networks using Quantitative Cellular Signatures

Handbook of Systems Biology

Volumn , Issue , 2013, Pages 89-113

  Kulkarni, Meghana M ^a   Perrimon, Norbert ^b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84882882757     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-385944-0.00005-8     Document Type: Chapter

References (274)

1. Pawson T. Protein modules and signaling networks. Nature 1995, 373:573-580.
2. Noselli S., Perrimon N. Signal transduction. Are there close encounters between signaling pathways?. Science 2000, 290:68-69.
3. Hou S.X., Zheng Z., Chen X., Perrimon N. The Jak/STAT pathway in model organisms: emerging roles in cell movement. Dev Cell 2002, 3:765-778.
4. Thomas J.H. Thinking about genetic redundancy. Trends Genet 1993, 9:395-399.
5. Perrimon N., Pitsouli C., Shilo B.-Z. Signaling mechanisms controlling cell fate and patterning. Cold Spring Harb Perspect Biol 2012, 4(8). pii: a005975.
6. Noselli S., Agnes F. Roles of the JNK signaling pathway in Drosophila morphogenesis. Curr Opin Genet Dev 1999, 9:466-472.
7. Lum L., Yao S., Mozer B., Rovescalli A., Von Kessler D., Nirenberg M., et al. Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells. Science 2003, 299:2039-2045.
8. Varelas X., Miller B.W., Sopko R., Song S., Gregorieff A., Fellouse F.A., et al. The Hippo pathway regulates Wnt/beta-catenin signaling. Dev Cell 2010, 18:579-591.
9. Xia L., Jia S., Huang S., Wang H., Zhu Y., Mu Y., et al. The Fused/Smurf complex controls the fate of Drosophila germline stem cells by generating a gradient BMP response. Cell 2010, 143:978-990.
10. Nusslein-Volhard C., Wieschaus E. Mutations affecting segment number and polarity in Drosophila. Nature 1980, 287:795-801.
11. Nusse R. Wnts and Hedgehogs: lipid-modified proteins and similarities in signaling mechanisms at the cell surface. Development 2003, 130:5297-5305.
12. Friedman A., Perrimon N. Genetic screening for signal transduction in the era of network biology. Cell 2007, 128:225-231.
13. Barabasi A.L., Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113.
14. Forster J., Famili I., Fu P., Palsson B.O., Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003, 13:244-253.
15. Han J.D., Bertin N., Hao T., Goldberg D.S., Berriz G.F., Zhang L.V., et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004, 430:88-93.
16. Deplancke B., Mukhopadhyay A., Ao W., Elewa A.M., Grove C.A., Martinez N.J., et al. A gene-centered C. elegans protein-DNA interaction network. Cell 2006, 125:1193-1205.
17. Watts D.J., Strogatz S.H. Collective dynamics of 'small-world' networks. Nature 1998, 393:440-442.
18. Barabasi A.L., Albert R. Emergence of scaling in random networks. Science 1999, 286:509-512.
19. Hahn M.W., Kern A.D. Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 2005, 22:803-806.
20. Jeong H., Mason S.P., Barabasi A.L., Oltvai Z.N. Lethality and centrality in protein networks. Nature 2001, 411:41-42.
21. Li S., Armstrong C.M., Bertin N., Ge H., Milstein S., Boxem M., et al. A map of the interactome network of the metazoan C. elegans. Science 2004, 303:540-543.
22. Albert R., Jeong H., Barabasi A.L. Error and attack tolerance of complex networks. Nature 2000, 406:378-382.
23. Toroczkai Z., Bassler K.E. Network dynamics: jamming is limited in scale-free systems. Nature 2004, 428:716.
24. Aldana M., Cluzel P. A natural class of robust networks. Proc Natl Acad Sci U S A 2003, 100:8710-8714.
25. Alon U. Network motifs: theory and experimental approaches. Nat Rev Genet 2007, 8:450-461.
26. Milo R., Shen-Orr S., Itzkovitz S., Kashtan N., Chklovskii D., Alon U. Network motifs: simple building blocks of complex networks. Science 2002, 298:824-827.
27. Davidson E.H. Network design principles from the sea urchin embryo. Curr Opin Genet Dev 2009, 19:535-540.
28. Pomerening J.R., Sontag E.D., Ferrell J.E. Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2. Nat Cell Biol 2003, 5:346-351.
29. Shen-Orr S.S., Milo R., Mangan S., Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 2002, 31:64-68.
30. Tyson J.J., Chen K.C., Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 2003, 15:221-231.
31. Wang R.S., Albert R. Elementary signaling modes predict the essentiality of signal transduction network components. BMC Syst Biol 2011, 5:44.
32. Yu H., Kim P.M., Sprecher E., Trifonov V., Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 2007, 3:e59.
33. Freeman L.C. A set of measures of centrality based on betweenness. Sociometry 1977, 40:35-41.
34. Girvan M., Newman M.E. Community structure in social and biological networks. Proc Natl Acad Sci U S A 2002, 99:7821-7826.
35. Joy M.P., Brock A., Ingber D.E., Huang S. High-betweenness proteins in the yeast protein interaction network. J Biomed Biotechnol 2005, 2005:96-103.
36. Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., et al. The genome sequence of Drosophila melanogaster. Science 2000, 287:2185-2195.
37. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
38. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., et al. The sequence of the human genome. Science 2001, 291:1304-1351.
39. Sharp P.A. RNAi and double-strand RNA. Genes Dev 1999, 13:139-141.
40. Newmark P.A. Opening a new can of worms: a large-scale RNAi screen in planarians. Dev Cell 2005, 8:623-624.
41. Newmark P.A., Reddien P.W., Cebria F., Sanchez Alvarado A. Ingestion of bacterially expressed double-stranded RNA inhibits gene expression in planarians. Proc Natl Acad Sci U S A 2003, 100(Suppl. 1):11861-11865.
42. Brodersen P., Voinnet O. The diversity of RNA silencing pathways in plants. Trends Genet 2006, 22:268-280.
43. Boutros M., Ahringer J. The art and design of genetic screens: RNA interference. Nat Rev Genet 2008, 9:554-566.
44. Echeverri C.J., Perrimon N. High-throughput RNAi screening in cultured cells: a user's guide. Nat Rev Genet 2006, 7:373-384.
45. Martin S.E., Caplen N.J. Applications of RNA interference in mammalian systems. Annu Rev Genomics Hum Genet 2007, 8:81-108.
46. Moffat J., Sabatini D.M. Building mammalian signaling pathways with RNAi screens. Nat Rev Mol Cell Biol 2006, 7:177-187.
47. Mohr S., Bakal C., Perrimon N. Genomic screening with RNAi: results and challenges. Annu Rev Biochem 2010, 79:37-64.
48. Perrimon N., Mathey-Prevot B. Applications of high-throughput RNA interference screens to problems in cell and developmental biology. Genetics 2007, 175:7-16.
49. Root D.E., Hacohen N., Hahn W.C., Lander E.S., Sabatini D.M. Genome-scale loss-of-function screening with a lentiviral RNAi library. Nat Methods 2006, 3:715-719.
50. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391:806-811.
51. Denli A.M., Hannon G.J. RNAi: an ever-growing puzzle. Trends Biochem Sci 2003, 28:196-201.
52. Hannon G.J. RNA interference. Nature 2002, 418:244-251.
53. Paddison P.J., Hannon G.J. RNA interference: the new somatic cell genetics?. Cancer Cell 2002, 2:17-23.
54. Perrimon N., Ni J.Q., Perkins L. In vivo RNAi: today and tomorrow. Cold Spring Harb Perspect Biol 2010, 2:a003640.
55. Clemens J.C., Worby C.A., Simonson-Leff N., Muda M., Maehama T., Hemmings B.A., et al. Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. Proc Natl Acad Sci U S A 2000, 97:6499-6503.
56. Hammond S.M., Boettcher S., Caudy A.A., Kobayashi R., Hannon G.J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 2001, 293:1146-1150.
57. Bernstein E., Caudy A.A., Hammond S.M., Hannon G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001, 409:363-366.
58. Bernstein E., Kim S.Y., Carmell M.A., Murchison E.P., Alcorn H., Li M.Z., et al. Dicer is essential for mouse development. Nat Genet 2003, 35:215-217.
59. Carmell M.A., Hannon G.J. RNase III enzymes and the initiation of gene silencing. Nat Struct Mol Biol 2004, 11:214-218.
60. Ketting R.F., Fischer S.E., Bernstein E., Sijen T., Hannon G.J., Plasterk R.H. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 2001, 15:2654-2659.
61. Nowotny M., Yang W. Structural and functional modules in RNA interference. Curr Opin Struct Biol 2009, 19:286-293.
62. Rao D.D., Vorhies J.S., Senzer N., Nemunaitis J. siRNA vs. shRNA: similarities and differences. Adv Drug Deliv Rev 2009, 61:746-759.
63. Tilesi F., Fradiani P., Socci V., Willems D., Ascenzioni F. Design and validation of siRNAs and shRNAs. Curr Opin Mol Ther 2009, 11:156-164.
64. Iorns E., Lord C.J., Turner N., Ashworth A. Utilizing RNA interference to enhance cancer drug discovery. Nat Rev Drug Discov 2007, 6:556-568.
65. Lord C.J., Martin S.A., Ashworth A. RNA interference screening demystified. J Clin Pathol 2009, 62:195-200.
66. Baeg G.H., Zhou R., Perrimon N. Genome-wide RNAi analysis of JAK/STAT signaling components in Drosophila. Genes Dev 2005, 19:1861-1870.
67. Bard F., Casano L., Mallabiabarrena A., Wallace E., Saito K., Kitayama H., et al. Functional genomics reveals genes involved in protein secretion and Golgi organization. Nature 2006, 439:604-607.
68. Boutros M., Kiger A.A., Armknecht S., Kerr K., Hild M., Koch B., et al. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 2004, 303:832-835.
69. DasGupta R., Kaykas A., Moon R.T., Perrimon N. Functional genomic analysis of the Wnt-wingless signaling pathway. Science 2005, 308:826-833.
70. Nybakken K., Vokes S.A., Lin T.Y., McMahon A.P., Perrimon N. A genome-wide RNA interference screen in Drosophila melanogaster cells for new components of the Hh signaling pathway. Nat Genet 2005, 37:1323-1332.
71. Li S., Wang L., Berman M.A., Zhang Y., Dorf M.E. RNAi screen in mouse astrocytes identifies phosphatases that regulate NF-kappaB signaling. Mol Cell 2006, 24:497-509.
72. Lu J., Ruhf M.L., Perrimon N., Leder P. A genome-wide RNA interference screen identifies putative chromatin regulators essential for E2F repression. Proc Natl Acad Sci U S A 2007, 104:9381-9386.
73. Mattila J., Kallijarvi J., Puig O. RNAi screening for kinases and phosphatases identifies FoxO regulators. Proc Natl Acad Sci U S A 2008, 105:14873-14878.
74. Kategaya L.S., Changkakoty B., Biechele T., Conrad W.H., Kaykas A., Dasgupta R., et al. Bili inhibits Wnt/beta-catenin signaling by regulating the recruitment of axin to LRP6. PLoS One 2009, 4:e6129.
75. Ma Y., Creanga A., Lum L., Beachy P.A. Prevalence of off-target effects in Drosophila RNA interference screens. Nature 2006, 443:359-363.
76. Tang W., Dodge M., Gundapaneni D., Michnoff C., Roth M., Lum L. A genome-wide RNAi screen for Wnt/beta-catenin pathway components identifies unexpected roles for TCF transcription factors in cancer. Proc Natl Acad Sci U S A 2008, 105:9697-9702.
77. Muller P., Kuttenkeuler D., Gesellchen V., Zeidler M.P., Boutros M. Identification of JAK/STAT signaling components by genome-wide RNA interference. Nature 2005, 436:871-875.
78. Ding L., Paszkowski-Rogacz M., Nitzsche A., Slabicki M.M., Heninger A.K., de Vries I., et al. A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. Cell Stem Cell 2009, 4:403-415.
79. Hu G., Kim J., Xu Q., Leng Y., Orkin S.H., Elledge S.J. A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev 2009, 23:837-848.
80. DasGupta R., Nybakken K., Booker M., Mathey-Prevot B., Gonsalves F., Changkakoty B., et al. A case study of the reproducibility of transcriptional reporter cell-based RNAi screens in Drosophila. Genome Biol 2007, 8:R203.
81. Dietzl G., Chen D., Schnorrer F., Su K.C., Barinova Y., Fellner M., et al. A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature 2007, 448:151-156.
82. Ni J.Q., Liu L.P., Binari R., Hardy R., Shim H.S., Cavallaro A., et al. A Drosophila resource of transgenic RNAi lines for neurogenetics. Genetics 2009, 182:1089-1100.
83. Mummery-Widmer J.L., Yamazaki M., Stoeger T., Novatchkova M., Bhalerao S., Chen D., et al. Genome-wide analysis of Notch signaling in Drosophila by transgenic RNAi. Nature 2009, 458:987-992.
84. Friedman A.A., Tucker G., Singh R., Yan D., Vinayagam A., Hu Y., et al. Proteomic and functional genomic landscape of receptor tyrosine kinase and Ras to extracellular signal-regulated kinase signaling. Science Signaling 2011, 4(196):rs10.
85. Friedman A., Perrimon N. A functional RNAi screen for regulators of receptor tyrosine kinase and ERK signaling. Nature 2006, 444:230-234.
86. Kockel L., Kerr K.S., Melnick M., Bruckner K., Hebrok M., Perrimon N. Dynamic switch of negative feedback regulation in Drosophila Akt-TOR signaling. PLoS Genet 2010, 6:e1000990.
87. Ziauddin J., Sabatini D.M. Microarrays of cells expressing defined cDNAs. Nature 2001, 411:107-110.
88. Mishina Y.M., Wilson C.J., Bruett L., Smith J.J., Stoop-Myer C., Jong S., et al. Multiplex GPCR assay in reverse transfection cell microarrays. J Biomol Screen 2004, 9:196-207.
89. Lindquist R.A., Ottina K.A., Wheeler D.B., Hsu P.P., Thoreen C.C., Guertin D.A., et al. Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1-S6K pathway signaling. Genome Res 2011, 21:433-446.
90. Carpenter A.E., Jones T.R., Lamprecht M.R., Clarke C., Kang I.H., Friman O., et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 2006, 7:R100.
91. Eggert U.S., Kiger A.A., Richter C., Perlman Z.E., Perrimon N., Mitchison T.J., et al. Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets. PLoS Biol 2004, 2:e379.
92. Loo L.H., Wu L.F., Altschuler S.J. Image-based multivariate profiling of drug responses from single cells. Nat Methods 2007, 4:445-453.
93. Paran Y., Ilan M., Kashman Y., Goldstein S., Liron Y., Geiger B., et al. High-throughput screening of cellular features using high-resolution light-microscopy; application for profiling drug effects on cell adhesion. J Struct Biol 2007, 158:233-243.
94. Perlman Z.E., Slack M.D., Feng Y., Mitchison T.J., Wu L.F., Altschuler S.J. Multidimensional drug profiling by automated microscopy. Science 2004, 306:1194-1198.
95. Rickardson L., Wickstrom M., Larsson R., Lovborg H. Image-based screening for the identification of novel proteasome inhibitors. J Biomol Screen 2007, 12:203-210.
96. Bakal C., Aach J., Church G., Perrimon N. Quantitative morphological signatures define local signaling networks regulating cell morphology. Science 2007, 316:1753-1756.
97. D'Ambrosio M.V., Vale R.D. A whole genome RNAi screen of Drosophila S2 cell spreading performed using automated computational image analysis. J Cell Biol 2010, 191:471-478.
98. Kiger A.A., Baum B., Jones S., Jones M.R., Coulson A., Echeverri C., et al. A functional genomic analysis of cell morphology using RNA interference. J Biol 2003, 2:27.
99. Moffat J., Grueneberg D.A., Yang X., Kim S.Y., Kloepfer A.M., Hinkle G., et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 2006, 124:1283-1298.
100. Goshima G., Wollman R., Goodwin S.S., Zhang N., Scholey J.M., Vale R.D., et al. Genes required for mitotic spindle assembly in Drosophila S2 cells. Science 2007, 316:417-421.
101. Mukherji M., Bell R., Supekova L., Wang Y., Orth A.P., Batalov S., et al. Genome-wide functional analysis of human cell-cycle regulators. Proc Natl Acad Sci U S A 2006, 103:14819-14824.
102. Collinet C., Stoter M., Bradshaw C.R., Samusik N., Rink J.C., Kenski D., et al. Systems survey of endocytosis by multiparametric image analysis. Nature 2010, 464:243-249.
103. Pelkmans L., Fava E., Grabner H., Hannus M., Habermann B., Krausz E., et al. Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis. Nature 2005, 436:78-86.
104. Agaisse H., Burrack L.S., Philips J.A., Rubin E.J., Perrimon N., Higgins D.E. Genome-wide RNAi screen for host factors required for intracellular bacterial infection. Science 2005, 309:1248-1251.
105. Cherry S., Doukas T., Armknecht S., Whelan S., Wang H., Sarnow P., et al. Genome-wide RNAi screen reveals a specific sensitivity of IRES-containing RNA viruses to host translation inhibition. Genes Dev 2005, 19:445-452.
106. Cherry S., Kunte A., Wang H., Coyne C., Rawson R.B., Perrimon N. COPI activity coupled with fatty acid biosynthesis is required for viral replication. PLoS Pathog 2006, 2:e102.
107. Philips J.A., Rubin E.J., Perrimon N. Drosophila RNAi screen reveals CD36 family member required for mycobacterial infection. Science 2005, 309:1251-1253.
108. Bai J., Binari R., Ni J.Q., Vijayakanthan M., Li H.S., Perrimon N. RNA interference screening in Drosophila primary cells for genes involved in muscle assembly and maintenance. Development 2008, 135:1439-1449.
109. Sepp K.J., Hong P., Lizarraga S.B., Liu J.S., Mejia L.A., Walsh C.A., et al. Identification of neural outgrowth genes using genome-wide RNAi. PLoS Genet 2008, 4:e1000111.
110. Vizeacoumar F.J., Chong Y., Boone C., Andrews B.J. A picture is worth a thousand words: genomics to phenomics in the yeast Saccharomyces cerevisiae. FEBS Lett 2009, 583:1656-1661.
111. Walter T., Shattuck D.W., Baldock R., Bastin M.E., Carpenter A.E., Duce S., et al. Visualization of image data from cells to organisms. Nat Methods 2010, 7:S26-41.
112. Bjorklund M., Taipale M., Varjosalo M., Saharinen J., Lahdenpera J., Taipale J. Identification of pathways regulating cell size and cell-cycle progression by RNAi. Nature 2006, 439:1009-1013.
113. Ramet M., Manfruelli P., Pearson A., Mathey-Prevot B., Ezekowitz R.A. Functional genomic analysis of phagocytosis and identification of a Drosophila receptor for E. coli. Nature 2002, 416:644-648.
114. Ulvila J., Parikka M., Kleino A., Sormunen R., Ezekowitz R.A., Kocks C., et al. Double-stranded RNA is internalized by scavenger receptor-mediated endocytosis in Drosophila S2 cells. J Biol Chem 2006, 281:14370-14375.
115. Kondo S., Perrimon N. A genome-wide RNAi screen identifies core components of the G-M DNA damage checkpoint. Sci Signal 2011, 4, rs1.
116. Ravi D., Wiles A.M., Bhavani S., Ruan J., Leder P., Bishop A.J. A network of conserved damage survival pathways revealed by a genomic RNAi screen. PLoS Genet 2009, 5:e1000527.
117. Wagner E.J., Burch B.D., Godfrey A.C., Salzler H.R., Duronio R.J., Marzluff W.F. A genome-wide RNA interference screen reveals that variant histones are necessary for replication-dependent histone pre-mRNA processing. Mol Cell 2007, 28:692-699.
118. Zhou R., Hotta I., Denli A.M., Hong P., Perrimon N., Hannon G.J. Comparative analysis of argonaute-dependent small RNA pathways in Drosophila. Mol Cell 2008, 32:592-599.
119. Feske S., Gwack Y., Prakriya M., Srikanth S., Puppel S.H., Tanasa B., et al. A mutation in Orai1 causes immune deficiency by abrogating CRAC channel function. Nature 2006, 441:179-185.
120. + entry. Science 2006, 312:1220-1223.
121. Zhang S.L., Yeromin A.V., Zhang X.H., Yu Y., Safrina O., Penna A., et al. Genome-wide RNAi screen of Ca(2+) influx identifies genes that regulate Ca(2+) release-activated Ca(2+) channel activity. Proc Natl Acad Sci U S A 2006, 103:9357-9362.
122. Zhang S., Binari R., Zhou R., Perrimon N. A genomewide RNA interference screen for modifiers of aggregates formation by mutant Huntingtin in Drosophila. Genetics 2010, 184:1165-1179.
123. Gandre-Babbe S., van der Bliek A.M. The novel tail-anchored membrane protein Mff controls mitochondrial and peroxisomal fission in mammalian cells. Mol Biol Cell 2008, 19:2402-2412.
124. Sathyanarayanan S., Zheng X., Kumar S., Chen C.H., Chen D., Hay B., et al. Identification of novel genes involved in light-dependent CRY degradation through a genome-wide RNAi screen. Genes Dev 2008, 22:1522-1533.
125. Dekanty A., Romero N.M., Bertolin A.P., Thomas M.G., Leishman C.C., Perez-Perri J.I., et al. Drosophila genome-wide RNAi screen identifies multiple regulators of HIF-dependent transcription in hypoxia. PLoS Genet 2010, 6:e1000994.
126. Kocks C., Cho J.H., Nehme N., Ulvila J., Pearson A.M., Meister M., et al. Eater, a transmembrane protein mediating phagocytosis of bacterial pathogens in Drosophila. Cell 2005, 123:335-346.
127. Foley E., O'Farrell P.H. Functional dissection of an innate immune response by a genome-wide RNAi screen. PLoS Biol 2004, 2:E203.
128. Gesellchen V., Kuttenkeuler D., Steckel M., Pelte N., Boutros M. An RNA interference screen identifies Inhibitor of Apoptosis Protein 2 as a regulator of innate immune signaling in Drosophila. EMBO Rep 2005, 6:979-984.
129. Kleino A., Valanne S., Ulvila J., Kallio J., Myllymaki H., Enwald H., et al. Inhibitor of apoptosis 2 and TAK1-binding protein are components of the Drosophila Imd pathway. EMBO J 2005, 24:3423-3434.
130. Bartscherer K., Pelte N., Ingelfinger D., Boutros M. Secretion of Wnt ligands requires Evi, a conserved transmembrane protein. Cell 2006, 125:523-533.
131. Gwack Y., Sharma S., Nardone J., Tanasa B., Iuga A., Srikanth S., et al. A genome-wide Drosophila RNAi screen identifies DYRK-family kinases as regulators of NFAT. Nature 2006, 441:646-650.
132. Dasgupta R., Perrimon N. Using RNAi to catch Drosophila genes in a web of interactions: insights into cancer research. Oncogene 2004, 23:8359-8365.
133. Gondi C.S., Rao J.S. Concepts in in vivo siRNA delivery for cancer therapy. J Cell Physiol 2009, 220:285-291.
134. Gondi C.S., Rao J.S. Therapeutic potential of siRNA-mediated targeting of urokinase plasminogen activator, its receptor, and matrix metalloproteinases. Methods Mol Biol 2009, 487:267-281.
135. Kim S.Y., Hahn W.C. Cancer genomics: integrating form and function. Carcinogenesis 2007, 28:1387-1392.
136. Wolters N.M., MacKeigan J.P. From sequence to function: using RNAi to elucidate mechanisms of human disease. Cell Death Differ 2008, 15:809-819.
137. Birmingham A., Anderson E.M., Reynolds A., Ilsley-Tyree D., Leake D., Fedorov Y., et al. 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods 2006, 3:199-204.
138. Jackson A.L., Linsley P.S. Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nat Rev Drug Discov 2010, 9:57-67.
139. Sigoillot F.D., King R.W. Vigilance and validation: Keys to success in RNAi screening. ACS Chem Biol 2011, 6:47-60.
140. Kulkarni M.M., Booker M., Silver S.J., Friedman A., Hong P., Perrimon N., et al. Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays. Nat Methods 2006, 3:833-838.
141. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
142. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
143. Brennecke J., Stark A., Russell R.B., Cohen S.M. Principles of microRNA-target recognition. PLoS Biol 2005, 3:e85.
144. Echeverri C.J., Beachy P.A., Baum B., Boutros M., Buchholz F., Chanda S.K., et al. Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat Methods 2006, 3:777-779.
145. Cherbas L., Willingham A., Zhang D., Yang L., Zou Y., Eads B.D., et al. The transcriptional diversity of 25 Drosophila cell lines. Genome Res 2011, 21:301-314.
146. Boone C., Bussey H., Andrews B.J. Exploring genetic interactions and networks with yeast. Nat Rev Genet 2007, 8:437-449.
147. Pan X., Yuan D.S., Xiang D., Wang X., Sookhai-Mahadeo S., Bader J.S., et al. A robust toolkit for functional profiling of the yeast genome. Mol Cell 2004, 16:487-496.
148. Tong A.H., Evangelista M., Parsons A.B., Xu H., Bader G.D., Page N., et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 2001, 294:2364-2368.
149. Tong A.H., Lesage G., Bader G.D., Ding H., Xu H., Xin X., et al. Global mapping of the yeast genetic interaction network. Science 2004, 303:808-813.
150. Bakal C., Linding R., Llense F., Heffern E., Martin-Blanco E., Pawson T., et al. Phosphorylation networks regulating JNK activity in diverse genetic backgrounds. Science 2008, 322:453-456.
151. Guertin D.A., Guntur K.V., Bell G.W., Thoreen C.C., Sabatini D.M. Functional genomics identifies TOR-regulated genes that control growth and division. Curr Biol 2006, 16:958-970.
152. Lehner B., Tischler J., Fraser A.G. RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions. Nat Protoc 2006, 1:1617-1620.
153. Wheeler D.B., Bailey S.N., Guertin D.A., Carpenter A.E., Higgins C.O., Sabatini D.M. RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells. Nat Methods 2004, 1:127-132.
154. Wheeler D.B., Carpenter A.E., Sabatini D.M. Cell microarrays and RNA interference chip away at gene function. Nat Genet 2005, 37(Suppl):S25-30.
155. Schuldiner M., Collins S.R., Thompson N.J., Denic V., Bhamidipati A., Punna T., et al. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 2005, 123:507-519.
156. Schuldiner M., Collins S.R., Weissman J.S., Krogan N.J. Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions. Methods 2006, 40:344-352.
157. Roguev A., Bandyopadhyay S., Zofall M., Zhang K., Fischer T., Collins S.R., et al. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science 2008, 322:405-410.
158. Horn T., Sandmann T., Fischer B., Axelsson E., Huber W., Boutros M. Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Nat Methods 2011, 8:341-346.
159. Chen H.W., Marinissen M.J., Oh S.W., Chen X., Melnick M., Perrimon N., et al. CKA, a novel multidomain protein, regulates the JUN N-terminal kinase signal transduction pathway in Drosophila. Mol Cell Biol 2002, 22:1792-1803.
160. Dreze M., Monachello D., Lurin C., Cusick M.E., Hill D.E., Vidal M., et al. High-quality binary interactome mapping. Methods Enzymol 2010, 470:281-315.
161. Fields S., Song O. A novel genetic system to detect protein- protein interactions. Nature 1989, 340:245-246.
162. Charbonnier S., Gallego O., Gavin A.C. The social network of a cell: recent advances in interactome mapping. Biotechnol Annu Rev 2008, 14:1-28.
163. Gingras A.C., Gstaiger M., Raught B., Aebersold R. Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol 2007, 8:645-654.
164. Kocher T., Superti-Furga G. Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat Methods 2007, 4:807-815.
165. Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 1999, 17:1030-1032.
166. Rain J.C., Selig L., De Reuse H., Battaglia V., Reverdy C., Simon S., et al. The protein-protein interaction map of Helicobacter pylori. Nature 2001, 409:211-215.
167. Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 2001, 98:4569-4574.
168. Ito T., Tashiro K., Muta S., Ozawa R., Chiba T., Nishizawa M., et al. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci U S A 2000, 97:1143-1147.
169. Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403:623-627.
170. Reboul J., Vaglio P., Rual J.F., Lamesch P., Martinez M., Armstrong C.M., et al. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet 2003, 34:35-41.
171. Walhout A.J., Sordella R., Lu X., Hartley J.L., Temple G.F., Brasch M.A., et al. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 2000, 287:116-122.
172. Formstecher E., Aresta S., Collura V., Hamburger A., Meil A., Trehin A., et al. Protein interaction mapping: a Drosophila case study. Genome Res 2005, 15:376-384.
173. Giot L., Bader J.S., Brouwer C., Chaudhuri A., Kuang B., Li Y., et al. A protein interaction map of Drosophila melanogaster. Science 2003, 302:1727-1736.
174. Stanyon C.A., Liu G., Mangiola B.A., Patel N., Giot L., Kuang B., et al. A Drosophila protein-interaction map centered on cell-cycle regulators. Genome Biol 2004, 5:R96.
175. Colland F., Jacq X., Trouplin V., Mougin C., Groizeleau C., Hamburger A., et al. Functional proteomics mapping of a human signaling pathway. Genome Res 2004, 14:1324-1332.
176. Lim J., Hao T., Shaw C., Patel A.J., Szabo G., Rual J.F., et al. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 2006, 125:801-814.
177. Rual J.F., Venkatesan K., Hao T., Hirozane-Kishikawa T., Dricot A., Li N., et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437:1173-1178.
178. Stelzl U., Worm U., Lalowski M., Haenig C., Brembeck F.H., Goehler H., et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122:957-968.
179. Venkatesan K., Rual J.F., Vazquez A., Stelzl U., Lemmens I., Hirozane-Kishikawa T., et al. An empirical framework for binary interactome mapping. Nat Methods 2009, 6:83-90.
180. von Mering C., Krause R., Snel B., Cornell M., Oliver S.G., Fields S., et al. Comparative assessment of large-scale data sets of protein- protein interactions. Nature 2002, 417:399-403.
181. Breitkreutz A., Choi H., Sharom J.R., Boucher L., Neduva V., Larsen B., et al. A global protein kinase and phosphatase interaction network in yeast. Science 2010, 328:1043-1046.
182. Gavin A.C., Aloy P., Grandi P., Krause R., Boesche M., Marzioch M., et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440:631-636.
183. Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415:141-147.
184. Ho Y., Gruhler A., Heilbut A., Bader G.D., Moore L., Adams S.L., et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415:180-183.
185. Krogan N.J., Cagney G., Yu H., Zhong G., Guo X., Ignatchenko A., et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440:637-643.
186. Puig O., Caspary F., Rigaut G., Rutz B., Bouveret E., Bragado-Nilsson E., et al. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 2001, 24:218-229.
187. Bouwmeester T., Bauch A., Ruffner H., Angrand P.O., Bergamini G., Croughton K., et al. A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol 2004, 6:97-105.
188. Major M.B., Roberts B.S., Berndt J.D., Marine S., Anastas J., Chung N., et al. New regulators of Wnt/beta-catenin signaling revealed by integrative molecular screening. Sci Signal 2008, 1, ra12.
189. Behrends C., Sowa M.E., Gygi S.P., Harper J.W. Network organization of the human autophagy system. Nature 2010, 466:68-76.
190. Sowa M.E., Bennett E.J., Gygi S.P., Harper J.W. Defining the human deubiquitinating enzyme interaction landscape. Cell 2009, 138:389-403.
191. Cloutier P., Al-Khoury R., Lavallee-Adam M., Faubert D., Jiang H., Poitras C., et al. High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes. Methods 2009, 48:381-386.
192. Glatter T., Wepf A., Aebersold R., Gstaiger M. An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol 2009, 5:237.
193. Calderwood M.A., Venkatesan K., Xing L., Chase M.R., Vazquez A., Holthaus A.M., et al. Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci U S A 2007, 104:7606-7611.
194. de Chassey B., Navratil V., Tafforeau L., Hiet M.S., Aublin-Gex A., Agaugue S., et al. Hepatitis C virus infection protein network. Mol Syst Biol 2008, 4:230.
195. Jager S., Gulbahce N., Cimermancic P., Kane J., He N., Chou S., et al. Purification and characterization of HIV-human protein complexes. Methods 2011, 53:13-19.
196. Shapira S.D., Gat-Viks I., Shum B.O., Dricot A., de Grace M.M., Wu L., et al. A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell. 2009, 139:1255-1267.
197. Uetz P., Dong Y.A., Zeretzke C., Atzler C., Baiker A., Berger B., et al. Herpesviral protein networks and their interaction with the human proteome. Science 2006, 311:239-242.
198. Tewari M., Hu P.J., Ahn J.S., Ayivi-Guedehoussou N., Vidalain P.O., Li S., et al. Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Mol Cell 2004, 13:469-482.
199. Ory S., Zhou M., Conrads T.P., Veenstra T.D., Morrison D.K. Protein phosphatase 2A positively regulates Ras signaling by dephosphorylating
200. Ritt D.A., Zhou M., Conrads T.P., Veenstra T.D., Copeland T.D., Morrison D.K. CK2 Is a component of the KSR1 scaffold complex that contributes to Raf kinase activation. Curr Biol 2007, 17:179-184.
201. Cuomo A., Bonaldi T. Systems biology 'on-the-fly': SILAC-based quantitative proteomics and RNAi approach in Drosophila melanogaster. Methods Mol Biol 2010, 662:59-78.
202. Selbach M., Mann M. Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK). Nat Methods 2006, 3:981-983.
203. Choudhary C., Mann M. Decoding signaling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol 2010, 11:427-439.
204. Ong S.E., Mann M. Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol 2005, 1:252-262.
205. Mann M. Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 2006, 7:952-958.
206. Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1:376-386.
207. Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3:1154-1169.
208. Thompson A., Schafer J., Kuhn K., Kienle S., Schwarz J., Schmidt G., et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 2003, 75:1895-1904.
209. DeRisi J., Penland L., Brown P.O., Bittner M.L., Meltzer P.S., Ray M., et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 1996, 14:457-460.
210. Roberts C.J., Nelson B., Marton M.J., Stoughton R., Meyer M.R., Bennett H.A., et al. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 2000, 287:873-880.
211. Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9:3273-3297.
212. Hsiao L.L., Dangond F., Yoshida T., Hong R., Jensen R.V., Misra J., et al. A compendium of gene expression in normal human tissues. Physiol Genomics 2001, 7:97-104.
213. Stuart J.M., Segal E., Koller D., Kim S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302:249-255.
214. Stolc V., Gauhar Z., Mason C., Halasz G., van Batenburg M.F., Rifkin S.A., et al. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 2004, 306:655-660.
215. Amit I., Garber M., Chevrier N., Leite A.P., Donner Y., Eisenhaure T., et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 2009, 326:257-263.
216. Ge H., Liu Z., Church G.M., Vidal M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 2001, 29:482-486.
217. Grigoriev A. A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res 2001, 29:3513-3519.
218. Jansen R., Greenbaum D., Gerstein M. Relating whole-genome expression data with protein-protein interactions. Genome Res 2002, 12:37-46.
219. Kemmeren P., van Berkum N.L., Vilo J., Bijma T., Donders R., Brazma A., et al. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol Cell 2002, 9:1133-1143.
220. Fambrough D., McClure K., Kazlauskas A., Lander E.S. Diverse signaling pathways activated by growth factor receptors induce broadly overlapping, rather than independent, sets of genes. Cell 1999, 97:727-741.
221. Greenbaum D., Colangelo C., Williams K., Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol 2003, 4:117.
222. Nie L., Wu G., Culley D.E., Scholten J.C., Zhang W. Integrative analysis of transcriptomic and proteomic data: challenges, solutions and applications. Crit Rev Biotechnol 2007, 27:63-75.
223. Dong M.Q., Venable J.D., Au N., Xu T., Park S.K., Cociorva D., et al. Quantitative mass spectrometry identifies insulin signaling targets in C. elegans. Science 2007, 317:660-663.
224. Janes K.A., Albeck J.G., Gaudet S., Sorger P.K., Lauffenburger D.A., Yaffe M.B. A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science 2005, 310:1646-1653.
225. Janes K.A., Reinhardt H.C., Yaffe M.B. Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell 2008, 135:343-354.
226. Miller-Jensen K., Janes K.A., Brugge J.S., Lauffenburger D.A. Common effector processing mediates cell-specific responses to stimuli. Nature 2007, 448:604-608.
227. Boulton S.J., Gartner A., Reboul J., Vaglio P., Dyson N., Hill D.E., et al. Combined functional genomic maps of the C. elegans DNA damage response. Science 2002, 295:127-131.
228. Piano F., Schetter A.J., Morton D.G., Gunsalus K.C., Reinke V., Kim S.K., et al. Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr Biol 2002, 12:1959-1964.
229. Boutros M., Agaisse H., Perrimon N. Sequential activation of signaling pathways during innate immune responses in Drosophila. Dev Cell 2002, 3:711-722.
230. Schena M., Shalon D., Davis R.W., Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470.
231. Hughes T.R., Marton M.J., Jones A.R., Roberts C.J., Stoughton R., Armour C.D., et al. Functional discovery via a compendium of expression profiles. Cell. 2000, 102:109-126.
232. Alizadeh A.A., Eisen M.B., Davis R.E., Ma C., Lossos I.S., Rosenwald A., et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403:503-511.
233. DeRisi J.L., Iyer V.R., Brown P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278:680-686.
234. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998, 95:14863-14868.
235. Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeek M., Mesirov J.P., et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537.
236. Gray N.S., Wodicka L., Thunnissen A.M., Norman T.C., Kwon S., Espinoza F.H., et al. Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors. Science 1998, 281:533-538.
237. Holstege F.C., Jennings E.G., Wyrick J.J., Lee T.I., Hengartner C.J., Green M.R., et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 1998, 95:717-728.
238. Marton M.J., DeRisi J.L., Bennett H.A., Iyer V.R., Meyer M.R., Roberts C.J., et al. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med 1998, 4:1293-1301.
239. Perou C.M., Jeffrey S.S., van de Rijn M., Rees C.A., Eisen M.B., Ross D.T., et al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci U S A 1999, 96:9212-9217.
240. van Wageningen S., Kemmeren P., Lijnzaad P., Margaritis T., Benschop J.J., de Castro I.J., et al. Functional overlap and regulatory links shape genetic interactions between signaling pathways. Cell 2010, 143:991-1004.
241. Lamb J. The Connectivity Map: a new tool for biomedical research. Nat Rev Cancer 2007, 7:54-60.
242. Lamb J., Crawford E.D., Peck D., Modell J.W., Blat I.C., Wrobel M.J., et al. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 2006, 313:1929-1935.
243. Hieronymus H., Lamb J., Ross K.N., Peng X.P., Clement C., Rodina A., et al. Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators. Cancer Cell 2006, 10:321-330.
244. Wei G., Twomey D., Lamb J., Schlis K., Agarwal J., Stam R.W., et al. Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance. Cancer Cell 2006, 10:331-342.
245. Ramaswamy S., Tamayo P., Rifkin R., Mukherjee S., Yeang C.H., Angelo M., et al. Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci U S A 2001, 98:15149-15154.
246. Su A.I., Cooke M.P., Ching K.A., Hakak Y., Walker J.R., Wiltshire T., et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A 2002, 99:4465-4470.
247. Su A.I., Wiltshire T., Batalov S., Lapp H., Ching K.A., Block D., et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 2004, 101:6062-6067.
248. Rhodes D.R., Yu J., Shanker K., Deshpande N., Varambally R., Ghosh D., et al. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia 2004, 6:1-6.
249. Stegmaier K., Ross K.N., Colavito S.A., O'Malley S., Stockwell B.R., Golub T.R. Gene expression-based high-throughput screening(GE-HTS) and application to leukemia differentiation. Nat Genet 2004, 36:257-263.
250. Hsuih T.C., Park Y.N., Zaretsky C., Wu F., Tyagi S., Kramer F.R., et al. Novel, ligation-dependent PCR assay for detection of hepatitis C in serum. J Clin Microbiol 1996, 34:501-507.
251. Landegren U., Kaiser R., Sanders J., Hood L. A ligase-mediated gene detection technique. Science 1988, 241:1077-1080.
252. Nilsson M., Barbany G., Antson D.O., Gertow K., Landegren U. Enhanced detection and distinction of RNA by enzymatic probe ligation. Nat Biotechnol 2000, 18:791-793.
253. Peck D., Crawford E.D., Ross K.N., Stegmaier K., Golub T.R., Lamb J. A method for high-throughput gene expression signature analysis. Genome Biol 2006, 7:R61.
254. Krutzik P.O., Nolan G.P. Intracellular phospho-protein staining techniques for flow cytometry: monitoring single cell signaling events. Cytometry A 2003, 55:61-70.
255. Perez O.D., Nolan G.P. Simultaneous measurement of multiple active kinase states using polychromatic flow cytometry. Nat Biotechnol 2002, 20:155-162.
256. Irish J.M., Hovland R., Krutzik P.O., Perez O.D., Bruserud O., Gjertsen B.T., et al. Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell 2004, 118:217-228.
257. Sachs K., Perez O., Pe'er D., Lauffenburger D.A., Nolan G.P. Causal protein-signaling networks derived from multiparameter single-cell data. Science 2005, 308:523-529.
258. Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., et al. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol 2002, 20:301-305.
259. Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R., Beausoleil S.A., et al. A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 2010, 143:1174-1189.
260. Wilson-Grady J.T., Villen J., Gygi S.P. Phosphoproteome analysis of fission yeast. J Proteome Res 2008, 7:1088-1097.
261. Yu Y., Anjum R., Kubota K., Rush J., Villen J., Gygi S.P. A site-specific, multiplexed kinase activity assay using stable-isotope dilution and high-resolution mass spectrometry. Proc Natl Acad Sci U S A 2009, 106:11606-11611.
262. Bodenmiller B., Wanka S., Kraft C., Urban J., Campbell D., Pedrioli P.G., et al. Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci Signal 2010, 3, rs4.
263. Ahrens C.H., Brunner E., Qeli E., Basler K., Aebersold R. Generating and navigating proteome maps using mass spectrometry. Nat Rev Mol Cell Biol 2010, 11:789-801.
264. Chen S.H., Albuquerque C.P., Liang J., Suhandynata R.T., Zhou H. A proteome-wide analysis of kinase-substrate network in the DNA damage response. J Biol Chem 2010, 285:12803-12812.
265. Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. Proc Natl Acad Sci U S A 2007, 104:10364-10369.
266. Tedford N.C., Hall A.B., Graham J.R., Murphy C.E., Gordon N.F., Radding J.A. Quantitative analysis of cell signaling and drug action via mass spectrometry-based systems level phosphoproteomics. Proteomics 2009, 9:1469-1487.
267. Przybylski C., Junger M.A., Aubertin J., Radvanyi F., Aebersold R., Pflieger D. Quantitative analysis of protein complex constituents and their phosphorylation states on a LTQ-Orbitrap instrument. J Proteome Res 2010, 9:5118-5132.
268. Hsu P.P., Kang S.A., Rameseder J., Zhang Y., Ottina K.A., Lim D., et al. The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science 2011, 332:1317-1322.
269. Yu Y., Yoon S.O., Poulogiannis G., Yang Q., Ma X.M., Villen J., et al. Phosphoproteomic analysis identifies Grb10 as an mTORC1 substrate that negatively regulates insulin signaling. Science 2011, 332:1322-1326.
270. Thoreen C.C., Kang S.A., Chang J.W., Liu Q., Zhang J., Gao Y., et al. An ATP-competitive mammalian target of rapamycin inhibitor reveals rapamycin-resistant functions of mTORC1. J Biol Chem 2009, 284:8023-8032.
271. Stratton M.R., Campbell P.J., Futreal P.A. The cancer genome. Nature 2009, 458:719-724.
272. Altshuler D., Daly M.J., Lander E.S. Genetic mapping in human disease. Science 2008, 322:881-888.
273. Geiss G.K., Bumgarner R.E., Birditt B., Dahl T., Dowidar N., Dunaway D.L., et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 2008, 26:317-325.
274. Kubota K., Anjum R., Yu Y., Kunz R.C., Andersen J.N., Kraus M., et al. Sensitive multiplexed analysis of kinase activities and activity-based kinase identification. Nat Biotechnol 2009, 27:933-940.