Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen

PLoS Computational Biology

Volumn 10, Issue 9, 2014, Pages

  Suratanee, Apichat ^a   Schaefer, Martin H ^b   Betts, Matthew J ^c   Soons, Zita ^d,e,f   Mannsperger, Heiko ^f   Harder, Nathalie ^c,f   Oswald, Marcus ^d,f,g   Gipp, Markus ^h   Ramminger, Ellen ⁱ   Marcus, Guillermo ^h   Männer, Reinhard ^h   Rohr, Karl ^c,f   Wanker, Erich ⁱ   Russell, Robert B ^c   Andrade Navarro, Miguel A ⁱ   Eils, Roland ^c,f   König, Rainer ^d,f,g  

^a KING MONGKUT'S UNIVERSITY OF TECHNOLOGY NORTH BANGKOK   (Thailand)

^b CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^c UNIVERSITY OF HEIDELBERG   (Germany)

^d HANS KNÖLL INSTITUTE   (Germany)

^e MAASTRICHT UNIVERSITY   (Netherlands)

^f GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^g JENA UNIVERSITY HOSPITAL   (Germany)

^h UNIVERSITY OF MANNHEIM   (Germany)

ⁱ MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CELL SIGNALING; CHEMICAL ACTIVATION; LANTHANUM COMPOUNDS; LEARNING SYSTEMS; PROTEINS; SIGNALING;

CELLULARS; COMPLEX SIGNALLING; GAIN INSIGHT; HELA CELL; INHIBITING EFFECT; PHENOTYPING; PROTEIN INTERACTION; PROTEIN-PROTEIN INTERACTIONS; SIGNALING SYSTEMS; SIGNALLING PATHWAYS;

GENES;

CHEMOKINE RECEPTOR CCR1; CHEMOKINE RECEPTOR CCR10; CHEMOKINE RECEPTOR CCR2; CHEMOKINE RECEPTOR CCR3; CHEMOKINE RECEPTOR CCR4; CHEMOKINE RECEPTOR CCR7; CHEMOKINE RECEPTOR CCR8; CHEMOKINE RECEPTOR CCR9; CHEMOKINE RECEPTOR CX3CR1; CHEMOKINE RECEPTOR CXCR4; CHEMOKINE RECEPTOR CXCR6; DISHEVELLED 2; GUANINE NUCLEOTIDE BINDING PROTEIN; JANUS KINASE 1; JANUS KINASE 2; JANUS KINASE 3; PROTEIN KINASE TYK2; SMALL INTERFERING RNA; SUPPRESSOR OF CYTOKINE SIGNALING; PROTEIN;

ARTICLE; CELL CULTURE; CLUSTER ANALYSIS; CONTROLLED STUDY; DISCRIMINANT ANALYSIS; DVL2 GENE; FZD7 GENE; GENE; GENE CLUSTER; GENE SILENCING; GENETIC ASSOCIATION; HELA CELL LINE; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; LINEAR DISCRIMINANT ANALYSIS; NONHUMAN; PHENOTYPE; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; RNA INTERFERENCE; SIGNAL TRANSDUCTION; SUPPORT VECTOR MACHINE; CHEMISTRY; GENETICS; GENOMICS; METABOLISM; PROCEDURES; PROTEIN DATABASE; RECEIVER OPERATING CHARACTERISTIC;

CLUSTER ANALYSIS; DATABASES, PROTEIN; GENE KNOCKDOWN TECHNIQUES; GENOMICS; HELA CELLS; HUMANS; PHENOTYPE; PROTEIN INTERACTION MAPS; PROTEINS; RNA, SMALL INTERFERING; ROC CURVE;

EID: 84907584445     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003814     Document Type: Article

References (33)

1. Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, et al. (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biol 8: R39.
2. Chuang HY, Lee E, Liu YT, Lee D, Ideker T, (2007) Network-based classification of breast cancer metastasis. Mol Syst Biol 3: 140.
3. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122: 957–968.
4. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480–484.
5. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human Protein Reference Database—2009 update. Nucleic Acids Res 37: D767–772.
6. Lage K, Mollgard K, Greenway S, Wakimoto H, Gorham JM, et al. (2010) Dissecting spatio-temporal protein networks driving human heart development and related disorders. Mol Syst Biol 6: 381.
7. Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, et al. (2010) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 39: D698–D704 doi: 10.1093/nar/gkq1116
8. Boutros M, Kiger AA, Armknecht S, Kerr K, Hild M, et al. (2004) Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 303: 832–835.
9. Harder N, Eils R, Rohr K, (2008) Automated classification of mitotic phenotypes of human cells using fluorescent proteins. Methods Cell Biol 85: 539–554.
10. Neumann B, Walter T, Heriche JK, Bulkescher J, Erfle H, et al. (2010) Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature 464: 721–727.
11. Bakal C, Aach J, Church G, Perrimon N, (2007) Quantitative morphological signatures define local signaling networks regulating cell morphology. Science 316: 1753–1756.
12. Fuchs F, Pau G, Kranz D, Sklyar O, Budjan C, et al. (2010) Clustering phenotype populations by genome-wide RNAi and multiparametric imaging. Mol Syst Biol 6: 370.
13. Vinayagam A, Zirin J, Roesel C, Hu Y, Yilmazel B, et al. (2014) Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. Nat Methods 11: 94–99.
14. Schaefer MH, Fontaine JF, Vinayagam A, Porras P, Wanker EE, et al. (2012) HIPPIE: Integrating protein interaction networks with experiment based quality scores. PLoS One 7: e31826.
15. Yang Y, (2003) Wnts and wing: Wnt signaling in vertebrate limb development and musculoskeletal morphogenesis. Birth Defects Res C Embryo Today 69: 305–317.
16. Chim CS, Pang R, Fung TK, Choi CL, Liang R, (2007) Epigenetic dysregulation of Wnt signaling pathway in multiple myeloma. Leukemia 21: 2527–2536.
17. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40: D290–301.
18. O'Sullivan LA, Liongue C, Lewis RS, Stephenson SEM, Ward AC, (2007) Cytokine receptor signaling through the Jak-Stat-Socs pathway in disease. Mol Immunol 44: 2497–2506.
19. Balkwill F, (2004) Cancer and the chemokine network. Nat Rev Cancer 4: 540–550.
20. Soriano SF, Serrano A, Hernanz-Falcon P, Martin de Ana A, Monterrubio M, et al. (2003) Chemokines integrate JAK/STAT and G-protein pathways during chemotaxis and calcium flux responses. Eur J Immunol 33: 1328–1333.
21. Wu B, Chien EY, Mol CD, Fenalti G, Liu W, et al. (2010) Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 330: 1066–1071.
22. Yoshimura A, Naka T, Kubo M, (2007) SOCS proteins, cytokine signalling and immune regulation. Nat Rev Immunol 7: 454–465.
23. Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, et al. (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics 26: 2347–2348.
24. Zhang Y, Tian L, Zheng Y, Qi H, Guo C, et al. (2011) C-terminal peptides of chemokine-like factor 1 signal through chemokine receptor CCR4 to cross-desensitize the CXCR4. Biochem Biophys Res Commun 409: 356–361.
25. Vinayagam A, Stelzl U, Foulle R, Plassmann S, Zenkner M, et al. (2011) A directed protein interaction network for investigating intracellular signal transduction. Sci Signal 4: rs8.
26. Sales G, Calura E, Cavalieri D, Romualdi C, (2012) graphite - a Bioconductor package to convert pathway topology to gene network. BMC Bioinformatics 13: 20.
27. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561–568.
28. Senger M, Flores T, Glatting K, Ernst P, Hotz-Wagenblatt A, et al. (1998) W2H: WWW interface to the GCG sequence analysis package. Bioinformatics 14: 452–457.
29. Senger M, Glatting KH, Ritter O, Suhai S, (1995) X-HUSAR, an X-based graphical interface for the analysis of genomic sequences. Comput Methods Programs Biomed 46: 131–141.
30. Yellaboina S, Tasneem A, Zaykin DV, Raghavachari B, Jothi R, (2011) DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic Acids Res 39: D730–735.
31. Chang CC, Lin CJ, (2001) LIBSVM: a library for support vector machines, Software available at http://www.csie.ntu.edu.tw/cjlin/-libsvm 80: 604–611.
32. Kranz AL, Eils R, König R, (2011) Enhancers regulate progression of development in mammalian cells. Nucleic Acids Res 39: 8689–8702.
33. Bauer T, Eils R, König R, (2011) RIP: the regulatory interaction predictor—a machine learning-based approach for predicting target genes of transcription factors. Bioinformatics 27: 2239–2247.