CoChat
Sign Up
Cited by 374

The DOI matches its Crossref record.

Conservation and divergence of gene families encoding components of innate immune response systems in zebrafish

Stein, Cornelia, Caccamo, Mario, Laird, Gavin, Leptin, Maria·2007·Genome Biology
DOI 10.1186/gb-2007-8-11-r251PMC PMC2258186
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1186/gb-2007-8-11-r251

Cites

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

No references could be resolved yet.

Research works printed but not linked: 56

  1. Trede NS, Langenau DM, Traver D, Look AT, Zon LI: The use of zebrafish to understand immunity. Immunity. 2004, 20: 367-379. 10.1016/S1074-7613(04)00084-6. · DOI
  2. Venkatesh B: Evolution and diversity of fish genomes. Curr Opin Genet Dev. 2003, 13: 588-592. 10.1016/j.gde.2003.09.001. · DOI
  3. Volff JN: Genome evolution and biodiversity in teleost fish. Heredity. 2005, 94: 280-294. 10.1038/sj.hdy.6800635. · DOI
  4. Traver D, Herbomel P, Patton EE, Murphey RD, Yoder JA, Litman GW, Catic A, Amemiya CT, Zon LI, Trede NS: The zebrafish as a model organism to study development of the immune system. Adv Immunol. 2003, 81: 253-330.
  5. Nonaka M, Kimura A: Genomic view of the evolution of the complement system. Immunogenetics. 2006, 58: 701-713. · DOI
  6. Meijer AH, Gabby Krens SF, Medina Rodriguez IA, He S, Bitter W, Ewa Snaar-Jagalska B, Spaink HP: Expression analysis of the Toll-like receptor and TIR domain adaptor families of zebrafish. Mol Immunol. 2004, 40: 773-783. 10.1016/j.molimm.2003.10.003. · DOI
  7. Jault C, Pichon L, Chluba J: Toll-like receptor gene family and TIR-domain adapters in Danio rerio. Mol Immunol. 2004, 40: 759-771. 10.1016/j.molimm.2003.10.001. · DOI
  8. Litman GW, Hawke NA, Yoder JA: Novel immune-type receptor genes. Immunol Rev. 2001, 181: 250-259. 10.1034/j.1600-065X.2001.1810121.x. · DOI
  9. Yoder JA, Mueller MG, Wei S, Corliss BC, Prather DM, Willis T, Litman RT, Djeu JY, Litman GW: Immune-type receptor genes in zebrafish share genetic and functional properties with genes encoded by the mammalian leukocyte receptor cluster. Proc Natl Acad Sci USA. 2001, 98: 6771-6776. 10.1073/pnas.121101598. · DOI
  10. Yoder JA, Litman RT, Mueller MG, Desai S, Dobrinski KP, Montgomery JS, Buzzeo MP, Ota T, Amemiya CT, Trede NS, et al: Resolution of the novel immune-type receptor gene cluster in zebrafish. Proc Natl Acad Sci USA. 2004, 101: 15706-15711. 10.1073/pnas.0405242101. · DOI
  11. Panagos PG, Dobrinski KP, Chen X, Grant AW, Traver D, Djeu JY, Wei S, Yoder JA: Immune-related, lectin-like receptors are differentially expressed in the myeloid and lymphoid lineages of zebrafish. Immunogenetics. 2006, 58: 31-40. 10.1007/s00251-005-0064-3. · DOI
  12. Bobe J, Goetz FW: Molecular cloning and expression of a TNF receptor and two TNF ligands in the fish ovary. Comp Biochem Physiol B Biochem Mol Biol. 2001, 129: 475-481. 10.1016/S1096-4959(01)00353-0. · DOI
  13. Engelsma MY, Huising MO, van Muiswinkel WB, Flik G, Kwang J, Savelkoul HF, Verburg-van Kemenade BM: Neuroendocrine-immune interactions in fish: a role for interleukin-1. Vet Immunol Immunopathol. 2002, 87: 467-479. 10.1016/S0165-2427(02)00077-6. · DOI
  14. Zou J, Secombes CJ, Long S, Miller N, Clem LW, Chinchar VG: Molecular identification and expression analysis of tumor necrosis factor in channel catfish (Ictalurus punctatus). Dev Comp Immunol. 2003, 27: 845-858. 10.1016/S0145-305X(03)00085-5. · DOI
  15. Huising MO, Stet RJ, Savelkoul HF, Verburg-van Kemenade BM: The molecular evolution of the interleukin-1 family of cytokines; IL-18 in teleost fish. Dev Comp Immunol. 2004, 28: 395-413. 10.1016/j.dci.2003.09.005. · DOI
  16. Reboul J, Gardiner K, Monneron D, Uze G, Lutfalla G: Comparative genomic analysis of the interferon/interleukin-10 receptor gene cluster. Genome Res. 1999, 9: 242-250. · DOI
  17. Lutfalla G, Roest Crollius H, Stange-Thomann N, Jaillon O, Mogensen K, Monneron D: Comparative genomic analysis reveals independent expansion of a lineage-specific gene family in vertebrates: the class II cytokine receptors and their ligands in mammals and fish. BMC Genomics. 2003, 4: 29-10.1186/1471-2164-4-29. · DOI
  18. Levraud JP, Boudinot P, Colin I, Benmansour A, Peyrieras N, Herbomel P, Lutfalla G: Identification of the zebrafish IFN receptor: implications for the origin of the vertebrate IFN system. J Immunol. 2007, 178: 4385-4394. · DOI
  19. Baoprasertkul P, Peatman E, Somridhivej B, Liu Z: Toll-like receptor 3 and TICAM genes in catfish: species-specific expression profiles following infection with Edwardsiella ictaluri. Immunogenetics. 2006, 58: 817-830. 10.1007/s00251-006-0144-z. · DOI
  20. Ben J, Jabs EW, Chong SS: Genomic, cDNA and embryonic expression analysis of zebrafish IRF6, the gene mutated in the human oral clefting disorders Van der Woude and popliteal pterygium syndromes. Gene Expr Patterns. 2005, 5: 629-638. 10.1016/j.modgep.2005.03.002. · DOI
  21. Lewis RS, Ward AC: Conservation, duplication and divergence of the zebrafish stat5 genes. Gene. 2004, 338: 65-74. 10.1016/j.gene.2004.05.012. · DOI
  22. Oganesyan G, Saha SK, Guo B, He JQ, Shahangian A, Zarnegar B, Perry A, Cheng G: Critical role of TRAF3 in the Toll-like receptor-dependent and -independent antiviral response. Nature. 2006, 439: 208-211. 10.1038/nature04374. · DOI
  23. van der Sar AM, Stockhammer OW, van der Laan C, Spaink HP, Bitter W, Meijer AH: MyD88 innate immune function in a zebrafish embryo infection model. Infect Immun. 2006, 74: 2436-2441. 10.1128/IAI.74.4.2436-2441.2006. · DOI
  24. Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, et al: Ensembl 2006. Nucleic Acids Res. 2006, 34: D556-561. 10.1093/nar/gkj133. · DOI
  25. Sprague J, Doerry E, Douglas S, Westerfield M: The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research. Nucleic Acids Res. 2001, 29: 87-90. 10.1093/nar/29.1.87. · DOI
  26. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410. · DOI · Paper page
  27. Kumar S, Tamura K, Nei M: MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 2004, 5: 150-163. 10.1093/bib/5.2.150. · DOI
  28. Sullivan C, Postlethwait JH, Lage CR, Millard PJ, Kim CH: Evidence for evolving Toll-IL-1 receptor-containing adaptor molecule function in vertebrates. J Immunol. 2007, 178: 4517-4527. · DOI
  29. Miller DJ, Hemmrich G, Ball EE, Hayward DC, Khalturin K, Funayama N, Agata K, Bosch TC: The innate immune repertoire in cnidaria - ancestral complexity and stochastic gene loss. Genome Biol. 2007, 8: R59-10.1186/gb-2007-8-4-r59. · DOI
  30. Kedinger V, Alpy F, Tomasetto C, Thisse C, Thisse B, Rio MC: Spatial and temporal distribution of the traf4 genes during zebrafish development. Gene Expr Patterns. 2005, 5: 545-552. · DOI
  31. Krause CD, Pestka S: Evolution of the Class 2 cytokines and receptors, and discovery of new friends and relatives. Pharmacol Ther. 2005, 106: 299-346. 10.1016/j.pharmthera.2004.12.002. · DOI
  32. Altmann SM, Mellon MT, Distel DL, Kim CH: Molecular and functional analysis of an interferon gene from the zebrafish, Danio rerio. J Virol. 2003, 77: 1992-2002. 10.1128/JVI.77.3.1992-2002.2003. · DOI
  33. Igawa D, Sakai M, Savan R: An unexpected discovery of two interferon gamma-like genes along with interleukin (IL)-22 and -26 from teleost: IL-22 and -26 genes have been described for the first time outside mammals. Mol Immunol. 2006, 43: 999-1009. 10.1016/j.molimm.2005.05.009. · DOI
  34. Chen JY, You YK, Chen JC, Huang TC, Kuo CM: Organization and promoter analysis of the zebrafish (Danio rerio) interferon gene. DNA Cell Biol. 2005, 24: 641-650. 10.1089/dna.2005.24.641. · DOI
  35. Milev-Milovanovic I, Long S, Wilson M, Bengten E, Miller NW, Chinchar VG: Identification and expression analysis of interferon gamma genes in channel catfish. Immunogenetics. 2006, 58: 70-80. 10.1007/s00251-006-0081-x. · DOI
  36. Long S, Milev-Milovanovic I, Wilson M, Bengten E, Clem LW, Miller NW, Chinchar VG: Identification and expression analysis of cDNAs encoding channel catfish type I interferons. Fish Shellfish Immunol. 2006, 21: 42-59. 10.1016/j.fsi.2005.10.008. · DOI
  37. Zou J, Carrington A, Collet B, Dijkstra JM, Yoshiura Y, Bols N, Secombes C: Identification and bioactivities of IFN-gamma in rainbow trout Oncorhynchus mykiss: the first Th1-type cytokine characterized functionally in fish. J Immunol. 2005, 175: 2484-2494. · DOI
  38. Zou J, Yoshiura Y, Dijkstra JM, Sakai M, Ototake M, Secombes C: Identification of an interferon gamma homologue in Fugu, Takifugu rubripes. Fish Shellfish Immunol. 2004, 17: 403-409. 10.1016/j.fsi.2004.04.015. · DOI
  39. Long S, Wilson M, Bengten E, Bryan L, Clem LW, Miller NW, Chinchar VG: Identification of a cDNA encoding channel catfish interferon. Dev Comp Immunol. 2004, 28: 97-111. 10.1016/S0145-305X(03)00122-8. · DOI
  40. Robertsen B, Bergan V, Rokenes T, Larsen R, Albuquerque A: Atlantic salmon interferon genes: cloning, sequence analysis, expression, and biological activity. J Interferon Cytokine Res. 2003, 23: 601-612. 10.1089/107999003322485107. · DOI
  41. Zhang DC, Shao YQ, Huang YQ, Jiang SG: Cloning, characterization and expression analysis of interleukin-10 from the zebrafish (Danio rerio). J Biochem Mol Biol. 2005, 38: 571-576. · DOI
  42. Zou J, Clark MS, Secombes CJ: Characterisation, expression and promoter analysis of an interleukin 10 homologue in the puffer fish, Fugu rubripes. Immunogenetics. 2003, 55: 325-335. 10.1007/s00251-003-0580-y. · DOI
  43. Zou J, Tafalla C, Truckle J, Secombes CJ: Identification of a second group of type I IFNs in fish sheds light on IFN evolution in vertebrates. J Immunol. 2007, 179: 3859-3871. · DOI
  44. Damiano JS, Oliveira V, Welsh K, Reed JC: Heterotypic interactions among NACHT domains: implications for regulation of innate immune responses. Biochem J. 2004, 381: 213-219. 10.1042/BJ20031506. · DOI
  45. Koonin EV, Aravind L: The NACHT family: a new group of predicted NTPases implicated in apoptosis and MHC transcription activation. Trends Biochem Sci. 2000, 25: 223-224. 10.1016/S0968-0004(00)01577-2. · DOI
  46. van der Biezen EA, Jones JD: The NB-ARC domain: a novel signalling motif shared by plant resistance gene products and regulators of cell death in animals. Curr Biol. 1998, 8: R226-227. 10.1016/S0960-9822(98)70145-9. · DOI
  47. Hibino T, Loza-Coll M, Messier C, Majeske AJ, Cohen AH, Terwilliger DP, Buckley KM, Brockton V, Nair SV, Berney K, et al: The immune gene repertoire encoded in the purple sea urchin genome. Dev Biol. 2006, 300: 349-365. 10.1016/j.ydbio.2006.08.065. · DOI · Paper page
  48. Rast JP, Smith LC, Loza-Coll M, Hibino T, Litman GW: Genomic insights into the immune system of the sea urchin. Science. 2006, 314: 952-956. 10.1126/science.1134301. · DOI
  49. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. 10.1093/nar/22.22.4673. · DOI · Paper page
  50. Lespinet O, Wolf YI, Koonin EV, Aravind L: The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 2002, 12: 1048-1059. 10.1101/gr.174302. · DOI
  51. Waterhouse RM, Kriventseva EV, Meister S, Xi Z, Alvarez KS, Bartholomay LC, Barillas-Mury C, Bian G, Blandin S, Christensen BM, et al: Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes. Science. 2007, 316: 1738-1743. 10.1126/science.1139862. · DOI
  52. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987, 4: 406-425.
  53. Renauld JC: Class II cytokine receptors and their ligands: key antiviral and inflammatory modulators. Nat Rev Immunol. 2003, 3: 667-676. 10.1038/nri1153. · DOI
  54. Eddy SR: Profile hidden Markov models. Bioinformatics. 1998, 14: 755-763. 10.1093/bioinformatics/14.9.755. · DOI · Paper page
  55. Schuster-Bockler B, Schultz J, Rahmann S: HMM Logos for visualization of protein families. BMC Bioinformatics. 2004, 5: 7-10.1186/1471-2105-5-7. · DOI
  56. Clamp M, Cuff J, Searle SM, Barton GJ: The Jalview Java alignment editor. Bioinformatics. 2004, 20: 426-427. 10.1093/bioinformatics/btg430. · DOI

Cited by

Sorted by citations

Metadata

Authors
Stein, C., Caccamo, M., Laird, G., & Leptin, M.
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2007-11-27
Volume
8
Issue
11
ISSN
1474-760X
DOI
10.1186/gb-2007-8-11-r251
PMC
PMC2258186
Cited by
374
References
0
Language
en
Licence

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review