Functional Analysis of Genes
References
- [1] AGI: THE ARABIDOPSIS GENOME INITIATIVE. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000; 408: 796-815
- [2] ALTSCHUL SF, GISH W, MILLER W, MYERS EW, LIPMAN DJ. Basic local alignment search tool. J Mol Biol 1990; 215: 403-410.
- [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.
- [4] AMBROS V, CHEN X. The regulation of genes and genomes by small RNAs. Development 2007; 134: 1635-1641
- [5] BENSON DA, KARSCH-MIZRACHI I, LIPMAN DJ, OSTELL J, WHEELER LD. GenBank: update. Nucleic Acids Res 2005; 32: 23-26
- [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.
- [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
- [8] CHALMEL F, PRIMIG M. The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. BMC Bioinformatics 2008; 9: 86.
- [9] CHAVAN P, JOSHI K, PATWARDHAN B. DNA Microarrays in Herbal Drug Research. Evid Based Complement Alternat Med 2006; 3: 447-457.
- [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.
- [11] FILIPECKI M, MALEPSZY S. Unintended consequences of plant transformation: a molecular insight. J Appl Genet 2006; 47: 277-286
- [12] FUELLEN G. Homology and phylogeny and their automated inference. Naturwissenschaften 2008; 95: 469-481
- [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.
- [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.
- [15] GIBSON G. Microarrays in ecology and evolution: a preview. Molecular Ecology 2002; 11: 17-24
- [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: 3804-3807
- [17] GOGARTEN JP, OLENDZENSKI L. Orthologs, paralogs and genome comparisons. Current Opinion in Genetics and Development 1999; 9: 630-636
- [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: 82-84
- [19] GOWRI VS, SANDHYA S. Recent trends in remote homology detection: an Indian Medley. Bioinformation 2006; 3: 94-96
- [20] GÓRSKA M, KOWALSKI ML. Knock-out genowy- zastosowanie w badaniach medycznych. Alergia, Astma, Immunologia. 1997: 2: 162-169
- [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.
- [22] JOHNSON DS, MORTAZAVI A, MYERS RM, WOLD B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007; 316: 1497-1502.
- [23] KRYSAN PJ, YOUNG JC, SUSSMAN MR. T-DNA as an insertional mutagen in Arabidopsis. Plant Cel 1999; 11: 2283-2290
- [24] KUMAR L, FUTSCHIK M. Mfuzz: A software package for soft clustering of microarray data. Bioinformation 2007; 2: 5-7.
- [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.
- [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.
- [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
- [28] MACKIEWICZ P, BĄCZKOWSKI K, SOBCZYŃSKI M, CEBRAT S. Zagadka sierocych otwartych ramek odczytu (ORF-anów). Biotechnologia 2005; 70: 45-56.
- [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.
- [30] MARTINEAU HM, PYRAH IT. Review of the Application of RNA interference technology in the pharmaceutical industry. Toxicol Pathol 2007; 35: 327-336
- [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.
- [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.
- [33] NOWAKOWSKA JA. Detekcja ekspresji genów drzew leśnych za pomocą mikromacierzy DNA. Sylwan 2006; 4: 33-43
- [34] NUC P, NUC K. Produkcja rekombinowanych białek w Escherichia coli. Post Bioch 2006; 52: 448-456
- [35] PAPROCKA M, WOŁOSZYŃSKA M. Potranskrypcyjne wyciszanie genów u roślin. Kosmos 2004; 53: 193- 200
- [36] POPTSOVA MS, GOGARTEN JP. The power of phylogenetic approaches to detect horizontally transferred genes. BMC Evolutionary Biology 2007; 7:45
- [37] ROMAN I. Mikromacierze DNA- perspektywy wykorzystania w badaniach skuteczności i bezpieczeństwa stosowania leków. Post Bioch 2008; 54: 107-115
- [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.
- [39] SJÖLANDER K. Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics 2004; 20: 170-179
- [40] SORENSEN HP, MORTENSEN KK. Advanced genetic strategies for recombinant protein expression in Eschericha coli. J Biotechnol 2005; 115: 113-128
- [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
- [42] VANHECKE D, JANITZ M. Functional genomics using high-throughput RNA interference. Drug Discov Today 2005; 10: 205-212.
- [43] WIŚNIEWSKA A, FILIPECKI M. Wyciszanie genów jako strategia badania ich funkcji w roślinach. Post Biol Kom 2003; 30: 339-358
- [44] XIONG Q, QIU Y, GU W. PGMapper: a web-based tool linking phenotype to genes. Bioinformatics Advance Access 2008; 10: 1323.
DOI: https://doi.org/10.2478/v10052-010-0001-y | Journal eISSN: 2544-3577 (formerly 2080-2218)
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
Keywords:
Related subjects:
© 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.