Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms

BMC Bioinformatics

Volumn 10, Issue SUPPL. 4, 2009, Pages

  Lin, Xiaotong ^a   Liu, Mei ^a   Chen, Xue Wen ^a  

^a University of Kansas   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HIGH THROUGHPUT EXPERIMENTS; INTEGRATIVE ANALYSIS; INTEGRATIVE FRAMEWORK; LARGE SCALE EXPERIMENTS; MICROARRAY DATA SETS; PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTIONS; SIGNAL TRANSDUCTION PATHWAYS;

BAYESIAN NETWORKS; BIOLOGY; GENES; RELIABILITY ANALYSIS; SIGNAL TRANSDUCTION; THROUGHPUT;

PROTEINS;

ARTICLE; BAYES THEOREM; CAENORHABDITIS ELEGANS; COMPUTER MODEL; DNA MICROARRAY; DROSOPHILA MELANOGASTER; GENE EXPRESSION; HUMAN; HUMAN GENOME; NONHUMAN; PROTEIN PROTEIN INTERACTION; RELIABILITY; SACCHAROMYCES CEREVISIAE; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; BINDING SITE; BIOLOGY; CHEMISTRY; GENETICS; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN DATABASE; YEAST;

PROTEIN;

BAYES THEOREM; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; GENOME, HUMAN; HUMANS; PROTEIN INTERACTION MAPPING; PROTEINS; YEASTS;

EID: 65549124391     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S4-S5     Document Type: Article

References (66)

1. Kone BC Protein-protein interactions controlling nitric oxide synthases Acta Physiol Scand 2000, 168(1):27-31. 10.1046/j.1365-201x.2000.00629.x 10691776
2. Wang J Protein recognition by cell surface receptors: Physiological receptors versus virus interactions Trends Biochem Sci 2002, 27(3):122-126. 10.1016/S0968-0004(01)02038-2 11893508
3. Phizicky EM Fields S Protein-protein interactions: Methods for detection and analysis Microbiol Rev 1995, 59(1):94-123. 239356 7708014
4. Martzen MR McCraith SM Spinelli SL Torres FM Fields S Grayhack EJ Phizicky EM A biochemical genomics approach for identifying genes by the activity of their products Science 1999, 286(5442):1153-1155. 10.1126/ science.286.5442.1153 10550052
5. Fields S Song O A novel genetic system to detect protein-protein interactions Nature 1989, 340(6230):245-246. 10.1038/340245a0 2547163
6. Gavin AC Bosche M Krause R Grandi P Marzioch M Bauer A Schultz J Rick JM Michon AM Cruciat CM et al Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002, 415(6868):141-147. 10.1038/415141a 11805826
7. Ho Y Gruhler A Heilbut A Bader GD Moore L Adams SL Millar A Taylor P Bennett K Boutilier K et al Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 2002, 415(6868):180-183. 10.1038/415180a 11805837
8. Zhu H Bilgin M Bangham R Hall D Casamayor A Bertone P Lan N Jansen R Bidlingmaier S Houfek T et al Global analysis of protein activities using proteome chips Science 2001, 293(5537):2101-2105. 10.1126/ science.1062191 11474067
9. Bollag DM Gel-filtration chromatography Methods Mol Biol 1994, 36:1-9. 7535158
10. Mullaney BP Pallavicini MG Protein-protein interactions in hematology and phage display Exp Hematol 2001, 29(10):1136-1146. 10.1016/ S0301-472X(01)00693-2 11602315
11. Deane CM Salwinski L Xenarios I Eisenberg D Protein interactions: Two methods for assessment of the reliability of high throughput observations Mol Cell Proteomics 2002, 1(5):349-356. 10.1074/ mcp.M100037-MCP200 12118076
12. Mrowka R Patzak A Herzel H Is there a bias in proteome research? Genome research 2001, 11(12):1971-1973. 10.1101/gr.206701 11731485
13. Uetz P Giot L Cagney G Mansfield TA Judson RS Knight JR Lockshon D Narayan V Srinivasan M Pochart P et al A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 2000, 403(6770):623-627. 10.1038/35001009 10688190
14. Ito T Chiba T Ozawa R Yoshida M Hattori M Sakaki Y A comprehensive two-hybrid analysis to explore the yeast protein interactome Proceedings of the National Academy of Sciences of the United States of America 2001, 98(8):4569-4574. 31875 11283351 10.1073/pnas.061034498
15. Watts DJ Strogatz SH Collective dynamics of 'small-world' networks Nature 1998, 393(6684):440-442. 10.1038/30918 9623998
16. Barabasi AL Albert R Emergence of scaling in random networks Science 1999, 286(5439):509-512. 10.1126/science.286.5439.509 10521342
17. Jeong H Mason SP Barabasi AL Oltvai ZN Lethality and centrality in protein networks Nature 2001, 411(6833):41-42. 10.1038/35075138 11333967
18. Ravasz E Somera AL Mongru DA Oltvai ZN Barabasi AL Hierarchical organization of modularity in metabolic networks Science 2002, 297(5586):1551-1555. 10.1126/science.1073374 12202830
19. Wolf YI Karev G Koonin EV Scale-free networks in biology: New insights into the fundamentals of evolution? Bioessays 2002, 24(2):105-109. 10.1002/bies.10059 11835273
20. von Mering C Krause R Snel B Cornell M Oliver SG Fields S Bork P Comparative assessment of large-scale data sets of protein-protein interactions Nature 2002, 417(6887):399-403. 10.1038/nature750 12000970
21. Bader GD Hogue CW Analyzing yeast protein-protein interaction data obtained from different sources Nature biotechnology 2002, 20(10):991-997. 10.1038/nbt1002-991 12355115
22. Mewes HW Frishman D Guldener U Mannhaupt G Mayer K Mokrejs M Morgenstern B Munsterkotter M Rudd S Weil B MIPS: A database for genomes and protein sequences Nucleic acids research 2002, 30(1):31-34. 99165 11752246 10.1093/nar/30.1.31
23. Kemmeren P van Berkum NL Vilo J Bijma T Donders R Brazma A Holstege FC Protein interaction verification and functional annotation by integrated analysis of genome-scale data Mol Cell 2002, 9(5):1133-1143. 10.1016/ S1097-2765(02)00531-2 12049748
24. Deng M Sun F Chen T Assessment of the reliability of protein-protein interactions and protein function prediction Pacific Symposium on Biocomputing 2003:140-151. 12603024
25. Jansen R Greenbaum D Gerstein M Relating whole-genome expression data with protein-protein interactions Genome research 2002, 12(1):37-46. 155252 11779829 10.1101/gr.205602
26. Bader JS Chaudhuri A Rothberg JM Chant J Gaining confidence in high-throughput protein interaction networks Nature biotechnology 2004, 22(1):78-85. 10.1038/nbt924 14704708
27. Sprinzak E Sattath S Margalit H How reliable are experimental protein-protein interaction data? J Mol Biol 2003, 327(5):919-923. 10.1016/S0022-2836(03)00239-0 12662919
28. Saito R Suzuki H Hayashizaki Y Interaction generality, a measurement to assess the reliability of a protein-protein interaction Nucleic acids research 2002, 30(5):1163-1168. 101243 11861907 10.1093/nar/30.5.1163
29. Goldberg DS Roth FP Assessing experimentally derived interactions in a small world Proceedings of the National Academy of Sciences of the United States of America 2003, 100(8):4372-4376. 404686 12676999 10.1073/ pnas.0735871100
30. Pazos F Helmer-Citterich M Ausiello G Valencia A Correlated mutations contain information about protein-protein interaction J Mol Biol 1997, 271(4):511-523. 10.1006/jmbi.1997.1198 9281423
31. Dandekar T Snel B Huynen M Bork P Conservation of gene order: A fingerprint of proteins that physically interact Trends Biochem Sci 1998, 23(9):324-328. 10.1016/S0968-0004(98)01274-2 9787636
32. Enright AJ Iliopoulos I Kyrpides NC Ouzounis CA Protein interaction maps for complete genomes based on gene fusion events Nature 1999, 402(6757):86-90. 10.1038/47056 10573422
33. Marcotte EM Pellegrini M Ng HL Rice DW Yeates TO Eisenberg D Detecting protein function and protein-protein interactions from genome sequences Science 1999, 285(5428):751-753. 10.1126/science.285.5428.751 10427000
34. Huynen M Snel B Lathe W 3rd Bork P Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences Genome research 2000, 10(8):1204-1210. 310926 10958638 10.1101/ gr.10.8.1204
35. Goh CS Bogan AA Joachimiak M Walther D Cohen FE Co-evolution of proteins with their interaction partners J Mol Biol 2000, 299(2):283-293. 10.1006/ jmbi.2000.3732 10860738
36. Pazos F Valencia A Similarity of phylogenetic trees as indicator of protein-protein interaction Protein Eng 2001, 14(9):609-614. 10.1093/ protein/14.9.609 11707606
37. Ramani AK Marcotte EM Exploiting the co-evolution of interacting proteins to discover interaction specificity J Mol Biol 2003, 327(1):273-284. 10.1016/S0022-2836(03)00114-1 12614624
38. Sprinzak E Margalit H Correlated sequence-signatures as markers of protein-protein interaction J Mol Biol 2001, 311(4):681-692. 10.1006/ jmbi.2001.4920 11518523
39. Kim WK Park J Suh JK Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair Genome Inform 2002, 13:42-50. 14571373
40. Deng M Mehta S Sun F Chen T Inferring domain-domain interactions from protein-protein interactions Genome research 2002, 12(10):1540-1548. 187530 12368246 10.1101/gr.153002
41. Ng SK Zhang Z Tan SH Integrative approach for computationally inferring protein domain interactions Bioinformatics (Oxford, England) 2003, 19(8):923-929. 10.1093/bioinformatics/btg118 12761053
42. Chen XW Liu M Prediction of protein-protein interactions using random decision forest framework Bioinformatics (Oxford, England) 2005 21 24 4394 4400 10.1093/bioinformatics/bti721 16234318
43. Chen XW Liu M Domain Based Predictive Models for Protein-Protein Interaction Prediction Journal on Applied Signal Processing 2006
44. Chen Y Xu D Computational analyses of high-throughput protein-protein interaction data Curr Protein Pept Sci 2003, 49(3):159-181. 10.2174/ 1389203033487225 12769716
45. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT et al Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nature genetics 2000, 25(1):25-29. 10.1038/75556 10802651
46. Zhang LV Wong SL King OD Roth FP Predicting co-complexed protein pairs using genomic and proteomic data integration BMC bioinformatics 2004, 5:38 419405 15090078 10.1186/1471-2105-5-38
47. Zhong W Sternberg PW Genome-wide prediction of C. elegans genetic interactions Science 2006, 311(5766):1481-1484. 10.1126/science.1123287 16527984
48. Jansen R Yu H Greenbaum D Kluger Y Krogan NJ Chung S Emili A Snyder M Greenblatt JF Gerstein M A Bayesian networks approach for predicting protein-protein interactions from genomic data Science 2003, 302(5644):449-453 10.1126/science.1087361 14564010
49. Rhodes DR Tomlins SA Varambally S Mahavisno V Barrette T Kalyana-Sundaram S Ghosh D Pandey A Chinnaiyan AM Probabilistic model of the human protein-protein interaction network Nature biotechnology 2005, 23(8):951-959. 10.1038/nbt1103 16082366
50. Myers CL Robson D Wible A Hibbs MA Chiriac C Theesfeld CL Dolinski K Troyanskaya OG Discovery of biological networks from diverse functional genomic data Genome biology 2005, 6 (13):R114. 1414113 16420673 10.1186/ gb-2005-6-13-r114
51. Remm M Storm CE Sonnhammer EL Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J Mol Biol 2001, 314(5):1041-1052. 10.1006/jmbi.2000.5197 11743721
52. Stark C Breitkreutz BJ Reguly T Boucher L Breitkreutz A Tyers M BioGRID: a general repository for interaction datasets Nucleic acids research 2006, 34 Database :D535-539. 1347471 16381927 10.1093/nar/gkj109
53. Peri S Navarro JD Amanchy R Kristiansen TZ Jonnalagadda CK Surendranath V Niranjan V Muthusamy B Gandhi TK Gronborg M et al Development of human protein reference database as an initial platform for approaching systems biology in humans Genome research 2003, 13(10):2363-2371. 403728 14525934 10.1101/gr.1680803
54. Mishra GR Suresh M Kumaran K Kannabiran N Suresh S Bala P Shivakumar K Anuradha N Reddy R Raghavan TM et al Human protein reference database-2006 update Nucleic acids research 2006, 34 Database:D411-414 1347503 16381900 10.1093/nar/gkj141
55. Edgar R Domrachev M Lash AE Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic acids research 2002, 30(1):207-210. 99122 11752295 10.1093/nar/30.1.207
56. Barrett T Edgar R Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*Methods Mol Biol 2006, 338:175-190. 1619899 16888359
57. Storey JD Akey JM Kruglyak L Multiple locus linkage analysis of genomewide expression in yeast PLoS Biol 2005, 3(8):e267. 1180512 16035920 10.1371/journal.pbio.0030267
58. Yvert G Brem RB Whittle J Akey JM Foss E Smith EN Mackelprang R Kruglyak L Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors Nature genetics 2003, 35(1):57-64. 10.1038/ ng1222 12897782
59. Brem RB Yvert G Clinton R Kruglyak L Genetic dissection of transcriptional regulation in budding yeast Science 2002, 296(5568):752-755. 10.1126/science.1069516 11923494
60. Baugh LR Hill AA Claggett JM Hill-Harfe K Wen JC Slonim DK Brown EL Hunter CP The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo Development 2005, 132(8):1843-1854. 10.1242/dev.01782 15772128
61. McElwee JJ Schuster E Blanc E Thomas JH Gems D Shared transcriptional signature in Caenorhabditis elegans Dauer larvae and long-lived daf-2 mutants implicates detoxification system in longevity assurance J Biol Chem 2004, 279(43):44533-44543. 10.1074/jbc.M406207200 15308663
62. Reinke V Smith HE Nance J Wang J Van Doren C Begley R Jones SJ Davis EB Scherer S Ward S et al A global profile of germline gene expression in C. elegans Mol Cell 2000, 6(3):605-616. 10.1016/S1097-2765(00)00059-9 11030340
63. Sorensen JG Nielsen MM Kruhoffer M Justesen J Loeschcke V Full genome gene expression analysis of the heat stress response in Drosophila melanogaster Cell Stress Chaperones 2005, 10(4):312-328. 1283958 16333985 10.1379/CSC-128R1.1
64. Beckstead RB Lam G Thummel CS The genomic response to 20-hydroxyecdysone at the onset of Drosophila metamorphosis Genome biology 2005, 6(12):R99. 1414087 16356271 10.1186/gb-2005-6-12-r99
65. Heckerman D A Tutorial on Learning with Bayesian Networks Learnings in Graphical Models. Cambridge, MA: MIT Press Jordan M 1999
66. Chen XW Anantha G Wang X An effective structure learning method for constructing gene networks Bioinformatics (Oxford, England) 2006, 22(11):1367-1374. 10.1093/bioinformatics/btl090 16543279