Corrigendum: Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum (Genome Research (2014) 24 (1433-1444) DOI: 10.1101/gr.158980.113);Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum

Genome Research

Volumn 24, Issue 9, 2014, Pages 1433-1444

  Yamagishi, Junya ^a,b   Natori, Anna ^c   Tolba, Mohammed E M ^d   Mongan, Arthur E ^e   Sugimoto, Chihiro ^f   Katayama, Toshiaki ^c   Kawashima, Shuichi ^c   Makalowski, Wojciech ^g   Maeda, Ryuichiro ^b   Eshita, Yuki ^h   Tuda, Josef ^e   Suzuki, Yutaka ^c  

^a TOHOKU UNIVERSITY   (Japan)

^b OBIHIRO UNIVERSITY OF AGRICULTURE AND VETERINARY MEDICINE   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d ASSIUT UNIVERSITY   (Egypt)

^e SAM RATULANGI UNIVERSITY   (Indonesia)

^f HOKKAIDO UNIVERSITY   (Japan)

^g UNIVERSITY OF MÜNSTER   (Germany)

^h OITA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE LYSINE METHYLTRANSFERASE; INITIATION FACTOR 3; POLYADENYLIC ACID BINDING PROTEIN; TOLL LIKE RECEPTOR 2; TOLL LIKE RECEPTOR 4; TOLL LIKE RECEPTOR ADAPTOR MOLECULE 2; TRANSCRIPTOME; TUMOR NECROSIS FACTOR ALPHA; ANTIMALARIAL AGENT; DNA BINDING PROTEIN; JUND PROTEIN, HUMAN; NUCLEAR PROTEIN; PROTEIN C JUN; SIGNAL PEPTIDE; SIGNAL TRANSDUCING ADAPTOR PROTEIN; TICAM2 PROTEIN, HUMAN; TLR2 PROTEIN, HUMAN; TNFAIP3 PROTEIN, HUMAN;

ADULT; ARTICLE; CONTROLLED STUDY; DISEASE SEVERITY; DOWN REGULATION; FEMALE; GENE EXPRESSION; GENE ONTOLOGY; GENETIC ASSOCIATION; GENETIC VARIABILITY; HOST PARASITE INTERACTION; HUMAN; INDONESIAN; INNATE IMMUNITY; MAJOR CLINICAL STUDY; MALARIA FALCIPARUM; MALE; NUCLEOTIDE SEQUENCE; PROTEIN EXPRESSION; REGULATORY MECHANISM; RNA ANALYSIS; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; UPREGULATION; ADOLESCENT; CASE CONTROL STUDY; CHILD; DRUG RESISTANCE; EXPRESSED SEQUENCE TAG; GENETICS; GENOME; HUMAN GENOME; INFANT; MALARIA; METABOLISM; PATHOGENICITY; PLASMODIUM FALCIPARUM; PRESCHOOL CHILD; VIRULENCE;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; ADOLESCENT; ADULT; ANTIMALARIALS; CASE-CONTROL STUDIES; CHILD; CHILD, PRESCHOOL; DNA-BINDING PROTEINS; DRUG RESISTANCE; EXPRESSED SEQUENCE TAGS; FEMALE; GENOME, HUMAN; GENOME, PROTOZOAN; HOST-PARASITE INTERACTIONS; HUMANS; IMMUNITY, INNATE; INFANT; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; MALARIA; MALE; NUCLEAR PROTEINS; PLASMODIUM FALCIPARUM; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTO-ONCOGENE PROTEINS C-JUN; TOLL-LIKE RECEPTOR 2; TRANSCRIPTOME; VIRULENCE;

EID: 84907219447     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.240291.118     Document Type: Erratum

References (51)

1. AregawiM, Cibulskis RE, LynchM, Williams R, World Health Organization, Global Malaria Programme. 2011. World malaria report 2011. World Health Organization, Geneva.
2. Armour CD, Castle JC, Chen R, Babak T, Loerch P, Jackson S, Shah JK, Dey J, Rohl CA, Johnson JM, et al. 2009. Digital transcriptome profiling using selective hexamer priming for cDNA synthesis. Nat Methods 6: 647-649.
3. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
4. Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, et al. 2009. PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res 37: D539-D543.
5. Birve A, Sengupta AK, Beuchle D, Larsson J, Kennison JA, Rasmuson- Lestander A, Muller J. 2001. Su(z)12, a novel Drosophila Polycomb group gene that is conserved in vertebrates and plants. Development 128: 3371-3379.
6. Chuang TH, Ulevitch RJ. 2004. Triad3A, an E3 ubiquitin-protein ligase regulating Toll-like receptors. Nat Immunol 5: 495-502.
7. Coban C, Ishii KJ, Kawai T, Hemmi H, Sato S, Uematsu S, Yamamoto M, Takeuchi O, Itagaki S, Kumar N, et al. 2005. Toll-like receptor 9 mediates innate immune activation by the malaria pigment hemozoin. J Exp Med 201: 19-25.
8. Coban C, Ishii KJ, Horii T, Akira S. 2007. Manipulation of host innate immune responses by the malaria parasite. Trends Microbiol 15: 271-278.
9. Coban C, Igari Y, Yagi M, Reimer T, Koyama S, Aoshi T, Ohata K, Tsukui T, Takeshita F, Sakurai K, et al. 2010. Immunogenicity of whole-parasite vaccines against Plasmodium falciparum involvesmalarial hemozoin and host TLR9. Cell Host Microbe 7: 50-61.
10. Cosgrove MS, Patel A. 2010. Mixed lineage leukemia: a structure-function perspective of the MLL1 protein. FEBS J 277: 1832-1842.
11. Daily JP, Scanfeld D, Pochet N, Le Roch K, Plouffe D, Kamal M, Sarr O, Mboup S, Ndir O, Wypij D, et al. 2007. Distinct physiological states of Plasmodium falciparum in malaria-infected patients. Nature 450: 1091-1095.
12. Dinarello CA. 2000. Proinflammatory cytokines. Chest 118: 503-508.
13. Duraisingh MT, Cowman AF. 2005. Contribution of the pfmdr1 gene to antimalarial drug-resistance. Acta Trop 94: 181-190.
14. Fidock DA, Nomura T, Talley AK, Cooper RA, Dzekunov SM, Ferdig MT, Ursos LM, Sidhu AB, Naude B, Deitsch KW, et al. 2000. Mutations in the P. falciparum digestive vacuole transmembrane protein PfCRT and evidence for their role in chloroquine resistance. Mol Cell 6: 861-871.
15. Franklin BS, Parroche P, Ataide MA, Lauw F, Ropert C, de Oliveira RB, Pereira D, Tada MS, Nogueira P, da Silva LH, et al. 2009. Malaria primes the innate immune response due to interferon-g induced enhancement of toll-like receptor expression and function. Proc Natl Acad Sci 106: 5789-5794.
16. Fu Y, Ding Y, Zhou T, Fu X, Xu W. 2012. Plasmodium yoelii blood-stage primes macrophage-mediated innate immune response through modulation of toll-like receptor signalling. Malar J 11: 104.
17. Gentleman RC, Carey VJ, Bates DM, Bolstad B, DettlingM, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
18. Gilmore TD. 2006. Introduction to NF-kB: players, pathways, perspectives. Oncogene 25: 6680-6684.
19. Han C, Jin J, Xu S, Liu H, Li N, Cao X. 2010. Integrin CD11b negatively regulates TLR-triggered inflammatory responses by activating Syk and promoting degradation of MyD88 and TRIF via Cbl-b. Nat Immunol 11: 734-742.
20. Hartgers FC, Obeng BB, Voskamp A, Larbi IA, Amoah AS, Luty AJ, Boakye D, Yazdanbakhsh M. 2008. Enhanced Toll-like receptor responsiveness associated with mitogen-activated protein kinase activation in Plasmodium falciparum-infected children. Infect Immun 76: 5149-5157.
21. Hoffmann A, Natoli G, Ghosh G. 2006. Transcriptional regulation via the NF-kB signaling module. Oncogene 25: 6706-6716.
22. Isaev A. 2004. Introduction to mathematical methods in bioinformatics. Springer, New York.
23. Ito T, Amakawa R, Fukuhara S. 2002. Roles of toll-like receptors in natural interferon-producing cells as sensors in immune surveillance. Hum Immunol 63: 1120-1125.
24. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. 2012. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40: D109-D114.
25. Kawai T, Akira S. 2010. The role of pattern-recognition receptors in innate immunity: update on Toll-like receptors. Nat Immunol 11: 373-384.
26. Kishimoto T. 2006. Interleukin-6: discovery of a pleiotropic cytokine. Arthritis Res Ther (Suppl 2) 8: S2.
27. Krishnegowda G, Hajjar AM, Zhu J, Douglass EJ, Uematsu S, Akira S, Woods AS, Gowda DC. 2005. Induction of proinflammatory responses in macrophages by the glycosylphosphatidylinositols of Plasmodium falciparum: cell signaling receptors, glycosylphosphatidylinositol (GPI) structural requirement, and regulation of GPI activity. J Biol Chem 280: 8606-8616.
28. Kristiansen M, Graversen JH, Jacobsen C, Sonne O, Hoffman HJ, Law SK, Moestrup SK. 2001. Identification of the haemoglobin scavenger receptor. Nature 409: 198-201.
29. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
30. Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, O'Brien J, Djimde A, Doumbo O, Zongo I, et al. 2012. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature 487: 375-379.
31. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. 2010. The Genome Analysis Toolkit: aMapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303.
32. Miggin SM, O'Neill LA. 2006. New insights into the regulation of TLR signaling. J Leukoc Biol 80: 220-226.
33. Miotto O, Almagro-Garcia J, Manske M, Macinnis B, Campino S, Rockett KA, Amaratunga C, Lim P, Suon S, Sreng S, et al. 2013. Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia. Nat Genet 45: 648-655.
34. Moll K, Ljungstrom I, Perlmann H, Scherf A, Wahlgren M. 2008. Methods in malaria research, 5th ed., pp. 18-19. Malaria Research and Reference Reagent Resource Center (MR4), American Type Culture Collection, Manassas, VA.
35. Mu J, Myers RA, Jiang H, Liu S, Ricklefs S, Waisberg M, Chotivanich K, Wilairatana P, Krudsood S, White NJ, et al. 2010. Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs. Nat Genet 42: 268-271.
36. Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR, Bohme U, Lemieux J, Barrell B, Pain A, Berriman M, et al. 2010. New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Mol Microbiol 76: 12-24.
37. Pahl HL. 1999. Activators and target genes of Rel/NF-kB transcription factors. Oncogene 18: 6853-6866.
38. Palm NW, Medzhitov R. 2009. Pattern recognition receptors and control of adaptive immunity. Immunol Rev 227: 221-233.
39. Parroche P, Lauw FN, Goutagny N, Latz E, Monks BG, Visintin A, Halmen KA, Lamphier M, Olivier M, Bartholomeu DC, et al. 2007. Malaria hemozoin is immunologically inert but radically enhances innate responses by presenting malaria DNA to Toll-like receptor 9. Proc Natl Acad Sci 104: 1919-1924.
40. Price RN, Uhlemann AC, Brockman A, McGready R, Ashley E, Phaipun L, Patel R, Laing K, Looareesuwan S, White NJ, et al. 2004. Mefloquine resistance in Plasmodium falciparum and increased pfmdr1 gene copy number. Lancet 364: 438-447.
41. Rao N, Dodge I, Band H. 2002. The Cbl family of ubiquitin ligases: critical negative regulators of tyrosine kinase signaling in the immune system. J Leukoc Biol 71: 753-763.
42. Reed MB, Saliba KJ, Caruana SR, Kirk K, Cowman AF. 2000. Pgh1 modulates sensitivity and resistance to multiple antimalarials in Plasmodium falciparum. Nature 403: 906-909.
43. Rogier C, Commenges D, Trape JF. 1996. Evidence for an age-dependent pyrogenic threshold of Plasmodium falciparum parasitemia in highly endemic populations. Am J Trop Med Hyg 54: 613-619.
44. Sato T, Onai N, Yoshihara H, Arai F, Suda T, Ohteki T. 2009. Interferon regulatory factor-2 protects quiescent hematopoietic stem cells from type I interferon-dependent exhaustion. Nat Med 15: 696-700.
45. Sawasdikosol S, Pratt JC, Meng W, Eck MJ, Burakoff SJ. 2000. Adapting to multiple personalities: Cbl is also a RING finger ubiquitin ligase. Biochim Biophys Acta 1471: M1-M12.
46. Song HY, Rothe M, Goeddel DV. 1996. The tumor necrosis factor-inducible zinc finger protein A20 interacts with TRAF1/TRAF2 and inhibits NF-kB activation. Proc Natl Acad Sci 93: 6721-6725.
47. Takeuchi O, Akira S. 2010. Pattern recognition receptors and inflammation. Cell 140: 805-820.
48. Tamura K, Dudley J, NeiM, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
49. Tuda J, Mongan AE, Tolba ME, Imada M, Yamagishi J, Xuan X, Wakaguri H, Sugano S, Sugimoto C, Suzuki Y. 2011. Full-parasites: database of fulllength cDNAs of apicomplexa parasites, 2010 update. Nucleic Acids Res 39: D625-D631.
50. Vereecke L, Beyaert R, van Loo G. 2009. The ubiquitin-editing enzyme A20 (TNFAIP3) is a central regulator of immunopathology. Trends Immunol 30: 383-391.
51. Volkman SK, Sabeti PC, DeCaprio D, Neafsey DE, Schaffner SF, Milner DA Jr, Daily JP, Sarr O, Ndiaye D, Ndir O, et al. 2007. A genome-wide map of diversity in Plasmodium falciparum. Nat Genet 39: 113-119.