Inferring functional modules of protein families with probabilistic topic models

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Konietzny, Sebastian G A ^a   Dietz, Laura ^a   McHardy, Alice C ^a,b  

^a MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^b HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESS; CO-OCCURRENCE PATTERN; FUNCTIONAL CHARACTERIZATION; FUNCTIONAL INTERACTION; FUNCTIONAL MODULES; PARTIAL INFORMATION; PROBABILISTIC MODELING; PROBABILISTIC TOPIC MODELS;

BAYESIAN NETWORKS; GENES;

PROTEINS;

PROTEIN;

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CHEMISTRY; CLASSIFICATION; FLAGELLUM; GENETICS; GENOME; METABOLISM; PROKARYOTIC CELL; STATISTICAL MODEL;

BAYES THEOREM; FLAGELLA; GENOME; MODELS, GENETIC; MODELS, STATISTICAL; PROKARYOTIC CELLS; PROTEINS;

EID: 79955691000     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-141     Document Type: Article

References (57)

1. Rubin EM. Genomics of cellulosic biofuels. Nature 2008, 454:841-845. 10.1038/nature07190, 18704079.
2. Osterman A, Overbeek R. Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 2003, 7:238-251. 10.1016/S1367-5931(03)00027-9, 12714058.
3. Reed JL, Famili I, Thiele I, Palsson BO. Towards multidimensional genome annotation. Nat Rev Genet 2006, 7:130-141. 10.1038/nrg1769, 16418748.
4. Stein L. Genome annotation: from sequence to biology. Nat Rev Genet 2001, 2:493-503.
5. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 2007, 5:e16. 10.1371/journal.pbio.0050016, 1821046, 17355171.
6. CAFA Challenge: Critical Assessment of Function Annotations. 2011, http://biofunctionprediction.org/
7. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 1999, 96:4285-4288. 10.1073/pnas.96.8.4285, 16324, 10200254.
8. Aravind L. Guilt by association: contextual information in genome analysis. Genome Res 2000, 10:1074-1077. 10.1101/gr.10.8.1074, 10958625.
9. Goh CS, Bogan AA, Joachimiak M, Walther D, Cohen FE. Co-evolution of proteins with their interaction partners. J Mol Biol 2000, 299:283-293. 10.1006/jmbi.2000.3732, 10860738.
10. Jothi R, Przytycka TM, Aravind L. Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics 2007, 8:173. 10.1186/1471-2105-8-173, 1904249, 17521444.
11. Kensche PR, van Noort V, Dutilh BE, Huynen MA. Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface 2008, 5:151-170. 10.1098/rsif.2007.1047, 2405902, 17535793.
12. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N. The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA 1999, 96:2896-2901. 10.1073/pnas.96.6.2896, 15866, 10077608.
13. Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA. Protein interaction maps for complete genomes based on gene fusion events. Nature 1999, 402:86-90. 10.1038/47056, 10573422.
14. van Noort V, Snel B, Huynen MA. Predicting gene function by conserved co-expression. Trends Genet 2003, 19:238-242. 10.1016/S0168-9525(03)00056-8, 12711213.
15. McGuire AM, Church GM. Predicting regulons and their cis-regulatory motifs by comparative genomics. Nucleic Acids Res 2000, 28:4523-4530. 10.1093/nar/28.22.4523, 113887, 11071941.
16. von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA, Bork P. Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci USA 2003, 100:15428-15433. 10.1073/pnas.2136809100, 307584, 14673105.
17. von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res 2005, 33:D433-D437. 539959, 15608232.
18. Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature 1999, 402:C47-C52. 10.1038/35011540, 10591225.
19. Pereira-Leal JB, Enright AJ, Ouzounis CA. Detection of functional modules from protein interaction networks. Proteins 2004, 54:49-57.
20. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. A combined algorithm for genome-wide prediction of protein function. Nature 1999, 402:83-86. 10.1038/47048, 10573421.
21. Rentzsch R, Orengo CA. Protein function prediction - the power of multiplicity. Trends Biotechnol 2009, 27:210-219. 10.1016/j.tibtech.2009.01.002, 19251332.
22. Navlakha S, Schatz MC, Kingsford C. Revealing biological modules via graph summarization. J Comput Biol 2009, 16:253-264. 10.1089/cmb.2008.11TT, 19183002.
23. Zhang KX, Ouellette BFF. Pandora, a pathway and network discovery approach based on common biological evidence. Bioinformatics 2010, 26:529-535. 10.1093/bioinformatics/btp701, 2820679, 20031970.
24. Fortunato S. Community detection in graphs. Phys Rep 2010, 486:75-174.
25. Brohee S, van Helden J. Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 2006, 7:488. 10.1186/1471-2105-7-488, 1637120, 17087821.
26. Watanabe RLA, Morett E, Vallejo EE. Inferring modules of functionally interacting proteins using the Bond Energy Algorithm. BMC Bioinformatics 2008, 9:285. 10.1186/1471-2105-9-285, 2474619, 18559112.
27. Bostan B, Greiner R, Szafron D, Lu P. Predicting homologous signaling pathways using machine learning. Bioinformatics 2009, 25:2913-2920. 10.1093/bioinformatics/btp532, 19736253.
28. Dale JM, Popescu L, Karp PD. Machine learning methods for metabolic pathway prediction. BMC Bioinformatics 2010, 11:15. 10.1186/1471-2105-11-15, 20064214.
29. Fröhlich H, Fellmann M, Sültmann H, Poustka A, Beissbarth T. Predicting pathway membership via domain signatures. Bioinformatics 2008, 24:2137-2142. 10.1093/bioinformatics/btn403, 2553439, 18676972.
30. Sun J, Xu J, Liu Z, Liu Q, Zhao A, Shi T, Li Y. Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinformatics 2005, 21:3409-3415. 10.1093/bioinformatics/bti532, 15947018.
31. Janga SC, Diaz-Mejia JJ, Moreno-Hagelsieb G. Network-based function prediction and interactomics: The case for metabolic enzymes. Metab Eng 2010, 13:1-10.
32. Blei DM, Ng AY, Jordan MI. Latent Dirichlet Allocation. J Mach Learn Res 2003, 3:993-1022.
33. Aso T, Eguchi K. Predicting protein-protein relationships from literature using latent topics. Genome Inform 2009, 23:3-12.
34. Zheng B, McLean DC, Lu X. Identifying biological concepts from a protein-related corpus with a probabilistic topic model. BMC Bioinformatics 2006, 7:58. 10.1186/1471-2105-7-58, 1420333, 16466569.
35. Flaherty P, Giaever G, Kumm J, Jordan MI, Arkin AP. A latent variable model for chemogenomic profiling. Bioinformatics 2005, 21:3286-3293. 10.1093/bioinformatics/bti515, 15919724.
36. Friedberg I. Automated protein function prediction - the genomic challenge. Brief Bioinform 2006, 7:225-242. 10.1093/bib/bbl004, 16772267.
37. Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res 2010, 38:D190-D195. 10.1093/nar/gkp951, 2808932, 19900971.
38. Meyer F, Overbeek R, Rodriguez A. FIGfams: yet another set of protein families. Nucleic Acids Res 2009, 37:6643-6654. 10.1093/nar/gkp698, 2777423, 19762480.
39. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer ELL. The Pfam protein families database. Nucleic Acids Res 2002, 30:276-280. 10.1093/nar/30.1.276, 99071, 11752314.
40. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28:33-36. 10.1093/nar/28.1.33, 102395, 10592175.
41. Pereira M, Parente JA, Bataus LAM, das Dores de Paula Cardoso D, Soares RBA, de Almeida Soares CM. Chemotaxis and flagellar genes of Chromobacterium violaceum. Genet Mol Res 2004, 3:92-101.
42. Rajagopala SV, Titz B, Goll J, Parrish JR, Wohlbold K, McKevitt MT, Palzkill T, Mori H, Finley RL, Uetz P. The protein network of bacterial motility. Mol Syst Biol 2007, 3:128. 1943423, 17667950.
43. Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res 2001, 29:41-43. 10.1093/nar/29.1.41, 29844, 11125044.
44. Koonin EV, Mushegian AR, Bork P. Non-orthologous gene displacement. Trends Genet 1996, 12:334-336.
45. Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P. Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol 2003, 21:790-795. 10.1038/nbt834, 12794638.
46. Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P. Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proc Natl Acad Sci USA 2007, 104:13913-13918. 10.1073/pnas.0702636104, 1955820, 17717083.
47. Turnbaugh PJ, Gordon JI. An invitation to the marriage of metagenomics and metabolomics. Cell 2008, 134:708-713. 10.1016/j.cell.2008.08.025, 18775300.
48. Rogozin IB, Makarova KS, Wolf YI, Koonin EV. Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes. Brief Bioinform 2004, 5:131-149. 10.1093/bib/5.2.131, 15260894.
49. Suhre K, Claverie JM. FusionDB: a database for in-depth analysis of prokaryotic gene fusion events. Nucleic Acids Res 2004, 32:D273-276. 10.1093/nar/gkh053, 308787, 14681411.
50. Liu Y, Harrison PM, Kunin V, Gerstein M. Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol 2004, 5:R64. 10.1186/gb-2004-5-9-r64, 522871, 15345048.
51. Vermunt JKMJ. Latent Class Cluster Analysis 2002, Cambridge University Press, Cambridge.
52. Blei DM, Griffiths TL, Jordan MI. The nested Chinese restaurant process and Bayesian nonparametric inference of topic hierarchies. J Acm 2010, 57:1-30.
53. Teh YW, Jordan MI, Beal MJ, Blei DM. Hierarchical Dirichlet processes. J Am Stat Assoc 2006, 101:1566-1581.
54. Gilks WR, Richardson S, Spiegelhalter DJ. Markov Chain Monte Carlo In Practice 1999, Chapman & Hall, CRC Interdisciplinary Statistics Series.
55. Griffiths TL, Steyvers M. Finding scientific topics. Proc Natl Acad Sci USA 2004, 101(SUPPL 1):5228-5235. 387300, 14872004.
56. Steyvers M, Griffiths T. Latent semantic analysis: a road to meaning. 2006, Laurence Erlbaum, Landauer T, McNamara D, Dennis S, Kintsch W.
57. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34:D354-D357. 10.1093/nar/gkj102, 1347464, 16381885.