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Functional Analysis of Genes Cover

Functional Analysis of Genes

Medical Journal of Cell Biology
Volume 2 (2010): Issue 1 (January 2010)
By: Dorota Sitnicka,  Katarzyna Figurska and  Slawomir Orzechowski  
Open Access
|Oct 2014

References

  1. [1] AGI: THE ARABIDOPSIS GENOME INITIATIVE. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000; 408: 796-81510.1038/35048692
    Search in Google Scholar
  2. [2] ALTSCHUL SF, GISH W, MILLER W, MYERS EW, LIPMAN DJ. Basic local alignment search tool. J Mol Biol 1990; 215: 403-410.223171210.1016/S0022-2836(05)80360-2
    Open DOISearch in Google Scholar
  3. [3] ALTSCHUL SF, MADDEN TL, SCHAFFER AA, ZHANG J, ZHANG Z, MILLER W, LIPMAN DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389-3402.10.1093/nar/25.17.33891469179254694
    Open DOISearch in Google Scholar
  4. [4] AMBROS V, CHEN X. The regulation of genes and genomes by small RNAs. Development 2007; 134: 1635-16411740911810.1242/dev.00200617409118
    Open DOISearch in Google Scholar
  5. [5] BENSON DA, KARSCH-MIZRACHI I, LIPMAN DJ, OSTELL J, WHEELER LD. GenBank: update. Nucleic Acids Res 2005; 32: 23-2610.1093/nar/gkh04530877914681350
    Search in Google Scholar
  6. [6] BERNSTEIN E, CAUDY AA, HAMMOND SM, HANNON GJ. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001; 409: 363-366.1120174710.1038/3505311011201747
    Open DOISearch in Google Scholar
  7. [7] BĄCZKOWSKI K, MACKIEWICZ K, KOWALCZUK M, BANASZAK J, CEBRAT S. Od sekwencji do funkcji - poszukiwanie genów i ich adnotacje. Biotechnologia 2005; 3: 22-44
    Search in Google Scholar
  8. [8] CHALMEL F, PRIMIG M. The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. BMC Bioinformatics 2008; 9: 86.10.1186/1471-2105-9-8618254954237511818254954
    Open DOISearch in Google Scholar
  9. [9] CHAVAN P, JOSHI K, PATWARDHAN B. DNA Microarrays in Herbal Drug Research. Evid Based Complement Alternat Med 2006; 3: 447-457.10.1093/ecam/nel075169775517173108
    Search in Google Scholar
  10. [10] DANFORD T, ROLFE A, GOFFORD D. GSE: A comprehensive database system for the representation, retrieval and analysis of microarray data. Pacific Symposium on Biocomputing 2008; 13: 539-550.
    Search in Google Scholar
  11. [11] FILIPECKI M, MALEPSZY S. Unintended consequences of plant transformation: a molecular insight. J Appl Genet 2006; 47: 277-2861713289210.1007/BF0319463717132892
    Open DOISearch in Google Scholar
  12. [12] FUELLEN G. Homology and phylogeny and their automated inference. Naturwissenschaften 2008; 95: 469-48110.1007/s00114-008-0348-11828847118288471
    Open DOISearch in Google Scholar
  13. [13] FUJITA A, SATO JR, FERREIRA CE, SOGAYAR MC. GEDI: a user-friendly toolbox for analysis of large-scale gene expression data. BMC Bioinformatics 2007; 8: 457.10.1186/1471-2105-8-45718021455
    Open DOISearch in Google Scholar
  14. [14] GENTLEMAN RC, CAREY VJ, BATES DM, BOLSTAD B, DETTLING M, DUDOIT S, ELLIS B, GAUTIER L, GE Y, GENTRY J, HORNIK K, HOTHORN T, HUBER W, IACUS S, IRIZARRY R, LEISCH F, LI CH, MAECHLER M, ROSSINI AJ, SAWITZKI G, SMITH C, SMYTH G, TIERNEY L, YANG JYH, ZHANG J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004; 5: R80.10.1186/gb-2004-5-10-r80
    Open DOISearch in Google Scholar
  15. [15] GIBSON G. Microarrays in ecology and evolution: a preview. Molecular Ecology 2002; 11: 17-2410.1046/j.0962-1083.2001.01425.x11903901
    Open DOISearch in Google Scholar
  16. [16] GINALSKI K, PAS J, WYRWICZ LS, GROTTHUSS M, BUJNICKI JM, RYCHLEWSKI L. ORFeus: detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Res 2003; 31: 3804-38071282442310.1093/nar/gkg504
    Open DOISearch in Google Scholar
  17. [17] GOGARTEN JP, OLENDZENSKI L. Orthologs, paralogs and genome comparisons. Current Opinion in Genetics and Development 1999; 9: 630-63610.1016/S0959-437X(99)00029-5
    Search in Google Scholar
  18. [18] GOLIAS CH, CHARALABOPOULOS A, STAGIKAS D, GIANNAKOPOULOS X, PESCHOS D, BATISTATOU A, SOFIKITIS N, CHARALABOPOULOS K. Molecular profiling and genomic microarrays in prostate cancer. Exp Oncol 2007; 29: 82-8417704736
    Search in Google Scholar
  19. [19] GOWRI VS, SANDHYA S. Recent trends in remote homology detection: an Indian Medley. Bioinformation 2006; 3: 94-9610.6026/97320630001094189165817597865
    Open DOISearch in Google Scholar
  20. [20] GÓRSKA M, KOWALSKI ML. Knock-out genowy- zastosowanie w badaniach medycznych. Alergia, Astma, Immunologia. 1997: 2: 162-169
    Search in Google Scholar
  21. [21] HOFFMAN BG, JONES SJM. Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing. J Endocrinol 2009; 201: 1-13.10.1677/JOE-08-05261913661719136617
    Open DOISearch in Google Scholar
  22. [22] JOHNSON DS, MORTAZAVI A, MYERS RM, WOLD B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007; 316: 1497-1502.10.1126/science.11413191754086217540862
    Open DOISearch in Google Scholar
  23. [23] KRYSAN PJ, YOUNG JC, SUSSMAN MR. T-DNA as an insertional mutagen in Arabidopsis. Plant Cel 1999; 11: 2283-229010.1105/tpc.11.12.228314413610590158
    Open DOISearch in Google Scholar
  24. [24] KUMAR L, FUTSCHIK M. Mfuzz: A software package for soft clustering of microarray data. Bioinformation 2007; 2: 5-7.10.6026/9732063000200518084642213999118084642
    Open DOISearch in Google Scholar
  25. [25] LARKIN MA, BLACKSHIELDS G, BROWN NP, CHENNA R, MCGETTIGAN PA, MCWILLIAM H, VALENTIN F, WALLACE IM, WILM A, LOPEZ R, THOMPSON JD, GIBSON TJ, HIGGINS DG. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23: 2947-2948.10.1093/bioinformatics/btm404
    Search in Google Scholar
  26. [26] LAW JP, CLAUDEL-RENARD C, JOUBERT F, LOUW AI, BERGER DK. MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters. BMC Genomics 2008; 9: 105.1830776810.1186/1471-2164-9-105
    Open DOISearch in Google Scholar
  27. [27] MACIEJEWSKI H, KONARSKI Ł, JASIŃSKA A, DRATH M. Analiza danych z mikromacierzy DNA- metody, narzędzia. Journal Edited by Medical College- Jagiellonion University 2005; 1: 129-132
    Search in Google Scholar
  28. [28] MACKIEWICZ P, BĄCZKOWSKI K, SOBCZYŃSKI M, CEBRAT S. Zagadka sierocych otwartych ramek odczytu (ORF-anów). Biotechnologia 2005; 70: 45-56.
    Search in Google Scholar
  29. [29] MARTIN D, BRUN Ch, REMY E, MOUREN P, THIEFFRY D, JACQ B. GOToolBox: functional analysis of gene datasets based on gene ontology. Genome Biol 2004; 5: R101.10.1186/gb-2004-5-12-r101
    Open DOISearch in Google Scholar
  30. [30] MARTINEAU HM, PYRAH IT. Review of the Application of RNA interference technology in the pharmaceutical industry. Toxicol Pathol 2007; 35: 327-3361745508010.1080/01926230701197107
    Open DOISearch in Google Scholar
  31. [31] MERCHANT S, PROCHNIK S, VALLON O, HARRIS E, KARPOWICZ S, WITMAN G, TERRY A, SALAMOV A, FRITZ-LAYLIN LK, MARECHAL-DROUARD L, MARSHALL W, LIANG-HU Q, NELSON D, SANDERFOOT A, SPALDING M, KAPITONOV V, REN Q, FERIS, LINDQUIST E, SHAPIRO H, LUCAS S, GRIMWOOD J, SCHMUTZ J, CHLAMYDOMONAS ANNOTATION TEAM, JGI ANNOTATION TEAM, GRIGORIEV I, ROKHSAR D, GROSSMAN A. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 2007; 318: 245-251.10.1126/science.1143609
    Open DOISearch in Google Scholar
  32. [32] NISHIMURA K, ABE K, ISHIKAWA S, TSUTSUMI S, HIROTA K, ABURATANI H, HIROSE M. A PCA Based Method of Gene Expression Visual Analysis. Genome Informat 2003; 14: 346-347.
    Search in Google Scholar
  33. [33] NOWAKOWSKA JA. Detekcja ekspresji genów drzew leśnych za pomocą mikromacierzy DNA. Sylwan 2006; 4: 33-43
    Search in Google Scholar
  34. [34] NUC P, NUC K. Produkcja rekombinowanych białek w Escherichia coli. Post Bioch 2006; 52: 448-456
    Search in Google Scholar
  35. [35] PAPROCKA M, WOŁOSZYŃSKA M. Potranskrypcyjne wyciszanie genów u roślin. Kosmos 2004; 53: 193- 200
    Search in Google Scholar
  36. [36] POPTSOVA MS, GOGARTEN JP. The power of phylogenetic approaches to detect horizontally transferred genes. BMC Evolutionary Biology 2007; 7:451737623010.1186/1471-2148-7-45
    Open DOISearch in Google Scholar
  37. [37] ROMAN I. Mikromacierze DNA- perspektywy wykorzystania w badaniach skuteczności i bezpieczeństwa stosowania leków. Post Bioch 2008; 54: 107-115
    Search in Google Scholar
  38. [38] SCHMIDT D, WILSON MD, SPYROU CH, BROWN GD, HADFIELD J, ODOM DT. ChIP-seq: Using high-throughput sequencing to discover protein-DNA interactions. Methods 2009; 48 :240-248.1927593910.1016/j.ymeth.2009.03.001
    Open DOISearch in Google Scholar
  39. [39] SJÖLANDER K. Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics 2004; 20: 170-17910.1093/bioinformatics/bth02114734307
    Open DOISearch in Google Scholar
  40. [40] SORENSEN HP, MORTENSEN KK. Advanced genetic strategies for recombinant protein expression in Eschericha coli. J Biotechnol 2005; 115: 113-12810.1016/j.jbiotec.2004.08.004
    Open DOISearch in Google Scholar
  41. [41] SZWEYKOWSKA-KULIŃSKA Z, SZARZYŃSKA B. Nagroda Nobla 2006 za fundamentalne odkrycia w regulacji ekspresji genów u Eucariontów. Post Biol Kom 2007; 34: 3-13
    Search in Google Scholar
  42. [42] VANHECKE D, JANITZ M. Functional genomics using high-throughput RNA interference. Drug Discov Today 2005; 10: 205-212.1570853510.1016/S1359-6446(04)03352-5
    Open DOISearch in Google Scholar
  43. [43] WIŚNIEWSKA A, FILIPECKI M. Wyciszanie genów jako strategia badania ich funkcji w roślinach. Post Biol Kom 2003; 30: 339-358
    Search in Google Scholar
  44. [44] XIONG Q, QIU Y, GU W. PGMapper: a web-based tool linking phenotype to genes. Bioinformatics Advance Access 2008; 10: 1323.
    Search in Google Scholar
DOI: https://doi.org/10.2478/v10052-010-0001-y | Journal eISSN: 2544-3577
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Language: English
Page range: 1 - 16
Published on: Oct 15, 2014
Published by: Foundation for Cell Biology and Molecular Biology
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year
Keywords:
gene expression,
gene,
DNA chips,
microarray
Related subjects:
Life sciences,
Molecular biology,
Biochemistry

© 2014 Dorota Sitnicka, Katarzyna Figurska, Slawomir Orzechowski, published by Foundation for Cell Biology and Molecular Biology
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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