Assessing functional annotation transfers with inter-species conserved coexpression: Application to Plasmodium falciparum

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Bréhélin, Laurent ^a   Florent, Isabelle ^b   Gascuel, Olivier ^a   Maréchal, Éric ^c  

^a LIRMM   (France)

^b MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

^c UNIV GRENOBLE ALPES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME PROTEIN; PROTOZOAL PROTEIN;

ARTICLE; BIOGENESIS; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; DRUG TARGETING; GENE ANNOTATION; GENE CLUSTER; GENE EXPRESSION; GENE FUNCTION; MOLECULAR GENETICS; NONHUMAN; ORTHOLOGY; PLASMODIUM FALCIPARUM; RIBOSOME; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; SPECIES COMPARISON; TRANSCRIPTOMICS; ALGORITHM; BIOLOGICAL MODEL; BIOLOGY; CLUSTER ANALYSIS; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENETICS; GENOME; METHODOLOGY; NUCLEOTIDE SEQUENCE;

DROSOPHILA MELANOGASTER; PLASMODIUM FALCIPARUM;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOME, PROTOZOAN; MODELS, GENETIC; PLASMODIUM FALCIPARUM; PROTOZOAN PROTEINS; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA;

EID: 77249158974     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-35     Document Type: Article

References (47)

1. Tuteja R. Malaria - an overview. FEBS J 2007, 274(18):4670-4679. 10.1111/j.1742-4658.2007.05997.x, 17824953.
2. Yeh I, Altman R. Drug Targets for Plasmodium falciparum: a post-genomic review/survey. Mini Rev Med Chem 2006, 6(2):177-202. 10.2174/138955706775475957, 16472186.
3. Greenwood B, Fidock D, Kyle D, Kappe S, Alonso P, Collins F, Duffy P. Malaria: progress, perils, and prospects for eradication. J Clin Invest 2008, 118(4):1266-1276. 10.1172/JCI33996, 2276780, 18382739.
4. Gardner M, Hall N, Fung E, White O, Berriman M, Hyman R, Carlton J, Pain A, Nelson K, Bowman S, Paulsen I, James K, Eisen J, Rutherford K, Salzberg S, Craig A, Kyes S, Chan M, Nene V, Shallom S, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather M, Vaidya A, Martin D, Fairlamb A, Fraunholz M, Roos D, Ralph S, McFadden G, Cummings L, Subramanian G, Mungall C, Venter J, Carucci D, Hoffman S, Newbold C, Davis R, Fraser C, Barrell B. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002, 419(6906):498-511. 10.1038/nature01097, 12368864.
5. Adl S, Leander B, Simpson A, Archibald J, Anderson O, Bass D, Bowser S, Brugerolle G, Farmer M, Karpov S, Kolisko M, Lane C, Lodge D, Mann D, Meisterfeld R, Mendoza L, Moestrup O, Mozley-Standridge S, Smirnov A, Spiegel F. Diversity, nomenclature, and taxonomy of protists. Syst Biol 2007, 56(4):684-689. 10.1080/10635150701494127, 17661235.
6. Baldauf S. The deep roots of eukaryotes. Science 2003, 300(5626):1703-1706. 10.1126/science.1085544, 12805537.
7. Pizzi E, Frontali C. Low-complexity regions in Plasmodium falciparum proteins. Genome Res 2001, 11(2):218-229. 10.1101/gr.GR-1522R, 311019, 11157785.
8. Altschul S, Gish W, Miller W, Myers E, Lipman D. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
9. Bastien O, Roy S, Marechal E. Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions. C R Biol 2005, 328(5):445-453. 10.1016/j.crvi.2005.02.002, 15948633.
10. Sonnhammer E, Eddy S, Birney E, Bateman A, Durbin R. Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res 1998, 26:320-322. 10.1093/nar/26.1.320, 147209, 9399864.
11. Punta M, Ofran Y. The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PLoS Comput Biol 2008, 4(10).
12. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95(25):14863-14868. 10.1073/pnas.95.25.14863, 24541, 9843981.
13. Lockhart D, Winzeler E. Genomics, gene expression and DNA arrays. Nature 2000, 405(6788):827-836. 10.1038/35015701, 10866209.
14. Le Roch K, Zhou Y, Blair P, Grainger M, Moch J, Haynes J, Vega PDL, Holder A, Batalov S, Carucci D, Winzeler E. Discovery of gene function by expression profiling of the malaria parasite life cycle. Science 2003, 301(5639):1503-1508. 10.1126/science.1087025, 12893887.
15. Zhou Y, Ramachandran V, Kumar KA, Westenberger S, Refour P, Zhou B, Li F, Young JA, Chen K, Plouffe D, Henson K, Nussenzweig V, Carlton J, Vinetz JM, Duraisingh MT, Winzeler EA. Evidence-Based Annotation of the Malaria Parasite's Genome Using Comparative Expression Profiling. PLoS ONE 2008, 3(2):e1570. 10.1371/journal.pone.0001570, 2215772, 18270564.
16. Bréhélin L, Dufayard J, Gascuel O. PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data. BMC Bioinformatics 2008, 9:440. 10.1186/1471-2105-9-440, 2605471, 18925948.
17. van Noort V, Snel B, Huynen M. Predicting gene function by conserved co-expression. Trends Genet 2003, 19(5):238-242. 10.1016/S0168-9525(03)00056-8, 12711213.
18. Stuart J, Segal E, Koller D, Kim S. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302(5643):249-255. 10.1126/science.1087447, 12934013.
19. Dutilh B, Huynen M, Snel B. A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation. BMC Genomics 2006, 7.
20. Bozdech Z, Llinas M, Pulliam B, Wong E, Zhu J, DeRisi J. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1:E5. 10.1371/journal.pbio.0000005, 176545, 12929205.
21. Gasch A, Spellman P, Kao C, Carmel-Harel O, Eisen M, Storz G, Botstein D, Brown P. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 2000, 11(12):4241-4257. 15070, 11102521.
22. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9(12):3273-3297. 25624, 9843569.
23. Pilot F, Philippe J, Lemmers C, Chauvin J, Lecuit T. Developmental control of nuclear morphogenesis and anchoring by charleston, identified in a functional genomic screen of Drosophila cellularisation. Development 2006, 133(4):711-723. 10.1242/dev.02251, 16421189.
24. Kohonen T. Self-Organizing Maps 1997, Springer.
25. Lloyd S. Least squares quantization in PCM. IEEE Trans Info Theory 1982, IT-2:129-137.
26. Herwig R, Poustka AJ, Muller C, Bull C, Lehrach H, O'Brien J. Large-scale clustering of cDNA-fingerprinting data. Genome Research 1999, 9(11):1093-105. 10.1101/gr.9.11.1093, 310829, 10568749.
27. Rabiner LR. A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition. Proceedings of the IEEE 1989, 77(2):257-285.
28. Durbin R, Eddy S, Krogh A, Mitchison G. Biological sequence analysis probabilistic models of proteins and nucleic acids 1998, Cambridge University Press.
29. McLachlan G, Peel D. Finite mixture models 2000, John Wiley.
30. Barale J, Attal-Bonnefoy G, Brahimi K, Pereira DSL, Langsley G. Plasmodium falciparum asparagine and aspartate rich protein 2 is an evolutionary conserved protein whose repeats identify a new family of parasite antigens. Mol Biochem Parasitol 1997, 87(2):169-181. 10.1016/S0166-6851(97)00065-0, 9247928.
31. McCutchan T, van Spaendonk R, Janse C, Fang J, Waters A. Malaria Parasites: Genomes and Molecular, Regulation of rRNA transcription and processing during the Plasmodium life cycle 2004 chap. Biology, Caister Academic Press, Waters AP, Janse CJ.
32. Smits P, Smeitink J, Heuvel LP, Huynen M, Ettema T. Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucleic Acids Res 2007, 35(14):4686-4703. 10.1093/nar/gkm441, 1950548, 17604309.
33. Mishra P, Kumar A, Sharma A. Analysis of small nucleolar RNAs reveals unique genetic features in malaria parasites. BMC Genomics 2009, 10:68. 10.1186/1471-2164-10-68, 2656528, 19200392.
34. Bottger E. Antimicrobial agents targeting the ribosome: the issue of selectivity and toxicity - lessons to be learned. Cell Mol Life Sci 2007, 64(7-8):791-795. 10.1007/s00018-007-6431-5, 17429579.
35. Clough B, Strath M, Preiser P, Denny P, Wilson I. Thiostrepton binds to malarial plastid rRNA. FEBS Lett 1997, 406(1-2):123-125. 10.1016/S0014-5793(97)00241-X, 9109400.
36. Rogers M, Bukhman Y, McCutchan T, Draper D. Interaction of thiostrepton with an RNA fragment derived from the plastid-encoded ribosomal RNA of the malaria parasite. RNA 1997, 3(8):815-820. 1369527, 9257641.
37. Camps M, Arrizabalaga G, Boothroyd J. An rRNA mutation identifies the apicoplast as the target for clindamycin in Toxoplasma gondii. Mol Microbiol 2002, 43(5):1309-1318. 10.1046/j.1365-2958.2002.02825.x, 11918815.
38. Kiatfuengfoo R, Suthiphongchai T, Prapunwattana P, Yuthavong Y. Mitochondria as the site of action of tetracycline on Plasmodium falciparum. Mol Biochem Parasitol 1989, 34(2):109-115. 10.1016/0166-6851(89)90002-9, 2651921.
39. Yassin A, Mankin A. Potential new antibiotic sites in the ribosome revealed by deleterious mutations in RNA of the large ribosomal subunit. J Biol Chem 2007, 282(33):24329-24342. 10.1074/jbc.M703106200, 17591769.
40. Sidhu A, Sun Q, Nkrumah L, Dunne M, Sacchettini J, Fidock D. In vitro efficacy, resistance selection, and structural modeling studies implicate the malarial parasite apicoplast as the target of azithromycin. J Biol Chem 2007, 282(4):2494-2504. 10.1074/jbc.M608615200, 17110371.
41. Doerig C, Chakrabarti D. Malaria Parasites: Genomes and Molecular Biology, Cell cycle control in Plasmodium falciparum: a genomic perspective 2004 chap. Caister Academic Press, Waters AP, Janse CJ.
42. Tienda-Luna I, Yin Y, Carrion M, Huang Y, Cai H, Sanchez M, Wang Y. Inferring the skeleton cell cycle regulatory network of malaria parasite using comparative genomic and variational Bayesian approaches. Genetica 2008, 132(2):131-142. 10.1007/s10709-007-9155-4, 17562188.
43. Ward P, Equinet L, Packer J, Doerig C. Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote. BMC Genomics 2004, 5:79. 10.1186/1471-2164-5-79, 526369, 15479470.
44. Kappes B, Rohrbach P. Microtubule inhibitors as a potential treatment for malaria. Future Microbiol 2007, 2:409-423. 10.2217/17460913.2.4.409, 17683277.
45. Doerig C, Meijer L. Antimalarial drug discovery: targeting protein kinases. Expert Opin Ther Targets 2007, 11(3):279-290. 10.1517/14728222.11.3.279, 17298288.
46. Birkholtz L, van Brummelen AC, Clark K, Niemand J, Marechal E, Llinas M, Louw A. Exploring functional genomics for drug target and therapeutics discovery in Plasmodia. Acta Trop 2008, 105(2):113-123. 10.1016/j.actatropica.2007.10.013, 18083131.
47. Young J, Fivelman Q, Blair P, de la Vega P, Le Roch K, Zhou Y, Carucci D, Baker D, Winzeler E. The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification. Mol Biochem Parasitol 2005, 143:67-79. 10.1016/j.molbiopara.2005.05.007, 16005087.