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*Tel. 062-970-2485 / Fax. 062-970-3414 / E-mail. dhkim@gist.ac.kr,.,.. (1)? (2) 1. (URL) KoSBI (http://www.kosbi.or.kr) Receptor Tyrosine Kinase Consortium (http://receptorkinase.gsc.riken.

1 *Tel / Fax / . dhkim@gist.ac.kr,.,.. (1)? (2) 1. (URL) KoSBI ( Receptor Tyrosine Kinase Consortium ( Hepatocyte systems biology ( DopaNet ( Yeast Systems Biology Network ( Computational and Systems Biology Initiative ( Alliance for Cellular Signaling ( STKE ( Receptor Tyrosine Kinase,, 17

2 ? (3) (stability) (robustness)? (4)? 21. DNA omics - (high-throughput, HT),. (synthetic biology) ( 1).. omics. omics, omics. omics. 1. omics ) (genomics). omics (2)., RNA,. omics 1995 Haemophilus influenzae (1).., ( 1).. omics., ) (transcriptomics) RNA RNA. SAGE (3), (4), (5). ) (proteomics), 2. (6, 7). 18

3 .. 1. Omics. 1) 2) 3). ) (metabolomics) omics.. ) (, phenomics). (12, 13) RNAi. 2. omics omics omics,. omics - -. ) (localizomics). omics. ) (interactome) -DNA. ChIP-chip Myc, NF-kB, p53, CREB (8-11). ) -DNA. omics.. ( 2). -DNA. Bar-Joseph GRAM ChIP-chip -DNA 19

4 (14). )., omics.. ), omics,. omics,. COBRA (15). COBRA,, omics. 3. omics Omics,. omics (16) omics 2. Omics... gene ontology.. ( : HCNet, the heart and calcium functional network database, 20

5 (17). omics (18). omics. 99%,, omics. Enard (19). omics. Double strand (ds) RNA C elegans knockdown (KD) (20) RNA (RNAi) silencing,, (21). C. elegans dsrna ( bp) silencing,. dsrna ( : sirnas, shrnas, shrna-mirs) (21). RNAi library,,. (high throughput screening). 50 RNAi 10 (21-28). interference RNA (sirna) RNAi dsrna transfection (22,23). ( : primary cells) transfection. Mitocheck - drug-target validation. RNA polymerase III promoter short hairpin RNA (shrna), plasmid (21) nucleotide stemloop nuclease DICER sirna RNA-induced silencing complex (RISC) silencing. shrna plasmid transfection, (24,26,28). RNAi shrna. Micro RNA (mirna) RNA polymerase II primary polyadenylated RNAs (pri-mir- NAs), pri-mirna DROSHA nucleotide hairpin mirna (pre-mirna). pre-mirna DICER mirna, mir-30 mirna, sirna RISC silencing. sirna silencing (25,27). RNAi..,. RNAi,. transfection.. multi-well-plate-based RNAi RNAi microarray (21). RNAi silencing 21

6 ., luciferase-reporter assay,, (fluorescence resonance energy transfer, FRET),,.. Hit.. ihop, HARVESTER curation. top-down ( : epistasis ). 3. Affinity purification. - ( :, KoSBI). yeast two-hybrid affinity purification MASS (interactome) ( 3). BIND, HPRD,, (literature mining).. false positive 30-60%, false negative 40-80% (29,30).. crosslinking footprinting,, FRET, (fluorescence cross-correlation spectroscopy)..,.., (31). (32,33). (34). (dissociation constants). 22

7 .. (binding free energy) (K d ,.,. 14 ~10-5 M) (35) ( 4).,...., ,.. ( :, KoSBI) 23

2. two-hybrid URL affinity purification X- RCSB http://www.rcsb.org NMR Docking HADDOCK http://www.nmr.chem.uu.nl/haddock InterPReTS http://interprets.embl.de NetPhos http://www.cbs.dtu.

8 2. two-hybrid URL affinity purification X- RCSB NMR Docking HADDOCK InterPReTS NetPhos PhosphoELM ispot (interactome) (36,37). X- NMR. Docking, 5. MCell ( 2). ( (structural genomics). (homology modeling).. electron tomography 40. ribosome ( 5)... 24

,,,, (bistability) (oscillation).,.,,,,, (apoptosis) Receptor tyrosine kinase (RTK) (38-40). Epidermal growth factor (EGFR) (41).,. PC12 EGF nerve growth factor (NGF) mitogen-activated kinase (MAPK).

9 ,,,, (bistability) (oscillation).,.,,,,, (apoptosis) Receptor tyrosine kinase (RTK) (38-40). Epidermal growth factor (EGFR) (41).,. PC12 EGF nerve growth factor (NGF) mitogen-activated kinase (MAPK). EGF MAPK,, NGF MAPK (42,43). MAPK... post-translational modification. StochSim, BioNetGen, Moleculizer.. allostericity.. cycle cascade (44). kinase phosphatase. ( 6).. (ultrasensitivity). sigmoidal hyperbolic.... (feedback)., ( ) ( ) 25

10 7. b-adrenergic -. FB ( :, KoSBI)..,., (45) (46,47) ( 7). (robustness)... CDK1/CDC2 cyclin (multi-stability) (48).... (gradient)... endocytosis..,.,.. YSBN (Yeast Systems Biology Network) RTKC(Receptor Tyrosine Kinase Consortium), EUSYSBIO (European Systems Biology). KoSBI (Korean Systems Biology Initiative). eimbl (eimbl-sbl) - 26

11 eimbl-sbl,,. -.,,,,,,,, eimbl-sbl 2006 Summer School on Computational Biology. ( : eimbl, electronic International Molecular Biology Laboratory SSCB2006 : omics post-genomic..,,.,,.,.. 1. Fleischmann, R. D. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, (1995). 2. Liolios, K. et al. The genomes on line database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res. 34, D332-D334 (2006). 3. Li, L. & Akashi, K. Unraveling the molecular components and genetic blueprints of stem cells. Biotechniques 35, (2003). 4. Rhodes, D. R. & Chinnaiyan, A. M. Integrative analysis of the cancer transcriptome. Nature Genet. 37, S31- S37 (2005). 5. Jenner, R. G. & Young, R. A. Insights into host responses against pathogens from transcriptional profiling. Nature Rev. Microbiol. 3, (2005). 6. Yates, J. R. 3rd, et al. Proteomics of organelles and large cellular structures. Nature Rev. Mol. Cell Biol. 6, (2005). 7. Kuster, B. et al. Scoring proteomes with proteotypic peptide probes. Nature Rev. Mol. Cell Biol. 6, (2005). 8. Li, Z. et al. A global transcriptional regulatory role for c-myc in Burkitt s lymphoma cells. Proc. Natl Acad. Sci. USA 100, (2003). 9. Martone, R. et al. Distribution of NF-B-binding sites across human chromosome 22. Proc. Natl Acad. Sci. USA 100, (2003). 10. Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, (2004). 11. Zhang, X. et al. Genome-wide analysis of campresponse element binding protein occupancy, phosphorylation, and target gene activation in human tis- 27

12 sues. Proc. Natl Acad. Sci. USA 102, (2005). 12. Bochner, B. R. New technologies to assess genotype-phenotype relationships. Nature Rev. Genet. 4, (2003). 13. Bredel, M. & Jacoby, E. Chemogenomics: an emerging strategy for rapid target and drug discovery. Nature Rev. Genet. 5, (2004). 14. Bar-Joseph, Z. et al. Computational discovery of gene modules and regulatory networks. Nature Biotechnol. 21, (2003). 15. Price, N. D. et al. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature Rev. Microbiol. 2, (2004). 16. Begley, T. J. et al. Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping. Mol. Cell 16, (2004). 17. Gunsalus, K. C. et al. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 436, (2005). 18. Ippolito, J. E. et al. An integrated functional genomics and metabolomics approach for defining poor prognosis in human neuroendocrine cancers. Proc. Natl Acad. Sci. USA 102, (2005). 19. Enard, W. et al. Intra- and interspecific variation in primate gene expression patterns. Science 296, (2002). 20. Fire, A., et al. Potent and specific genetic interferance by double-stranded RNA in Caenorhabditis elegans. Nature 391, (1998) 21. Moffat, J & Sabatini, D.M. (2006) Building mammalian signalling pathways with RNAi screens. Nature Reviews 7: Elbashir, S.M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in culturedc mammalian cells. Nature 411, (2001) 23. Brummelkamp, T.R. et al. A system for stable expression of short interfering RNAs in mammalian cells. Science 296, (2002) 24. Berns, K. et al. A large-scale RNAi screen in human cells identifies new componets of the p53 pathway. Nature 428, (2004) 25. Dickins, R.A. et al. Probing tumor phenotypes using stable and regulated synthetic microrna precursors. Nature Genetics 37, (2005) 26. Pelkmans, L. et al. Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis. Nature 436, (2005) 27. Silva, J.M. et al. Second-generation shrna libraries covering the mouse and human genomes. Nature Gen. 37, (2005) 28. Moffat, J. et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral highcontent screen. Cell 124: (2006) 29. Joyce, A. R. & Palsson, B. The model organism as a system: integrating omics data sets. Nat. Rev. Mol. Cell. Bio. 7, (2006) 30. von Mering, C. et al. Comparative assessment of largescale data sets of protein-protein interactions. Nature 417, (2002). 31. Aloy, P. & Russell, R. B. Ten thousand interactions for the molecular biologist. Nature Biotechnol. 22, (2004). 32. Aloy, P. & Russell, R.B. Structural systems biology: modelling protein interactions. Nat. Rev. Mol. Cell. Biol. 7, (2006) 33. Jansen, R. et al. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302, (2003). 34. von Mering, C. et al. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 33, D433-D437 (2005). 35. Zhou, H. X. Association and dissociation kinetics of colicin E3 and immunity protein 3: convergence of theory and experiment. Protein Sci. 12, (2003). 36. Stelzl, U. et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, (2005). 37. Rual, J. F. et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, (2005). 38. Schlessinger, J. Cell signaling by receptor tyrosine kinases. Cell 103, (2000). 39. Hunter, T. Signaling and beyond. Cell 100, (2000). 40. Gray, S. G., Stenfeldt Mathiasen, I. & De Meyts, P. The insulin-like growth factors and insulin-signalling systems: an appealing target for breast cancer ther- 28

13 apy? Horm. Metab. Res. 35, (2003). 41. Schlessinger, J. Common and distinct elements in cellular signaling via EGF and FGF receptors. Science 306, (2004). 42. Marshall, C. J. Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation. Cell 80, (1995). 43. Murphy, L. O. et al. Molecular interpretation of ERK signal duration by immediate early gene products. Nature Cell Biol. 4, (2002). 44. Kholodenko, B. N., Cell-signalling dynamics in time and space. Nature Rev. Mol. Cell Biol. 7, (2006) 45. Goldbeter, A. Computational approaches to cellular rhythms. Nature 420, (2002). 46. Sha, W. et al. Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proc. Natl Acad. Sci. USA 100, (2003). 47. Pomerening, J. R. et al. Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2. Nature Cell Biol. 5, (2003). 48. Markevich, N. I. et al. Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J. Cell. Biol. 164, (2004). 29

System Biology Core

System Biology Core 연세의생명연구원연구지원부 _ 연세유전체센터 The RNAi Consortium (TRC) shrna 안내 Ⅰ. MISSION shrna 의설계 MIT 와 Harvard 의 Broad Institute 의 The RNAi Consortium (TRC) 에서설계하고개발한 MISSION shrna clones 는 21 base