Functional Genomics

Main Article Content

Huang Caihong
Yang Qian*

Abstract

Molecular biology has advanced a lot in recent years. So far, the complete genome sequences of several eukaryotes have been published. The first draft of the human genome has been completed ahead of schedule. Thus, much of the sequencing work is done. Now, the focus in genomic research is shifting from “structural genomics” towards “functional genomics” Functional genomics is a relatively new field of molecular biology that studies how genomic information defines the functions of proteins in living organism. It combines high-throughput experimental methodologies with statistical and statistical and computational analysis of the results to study genes or proteins in a systematic and systemic fashion. Study on bioinformatics is of crucial importance for our ability to exploit the wealth of information contained in the human genome for applied research. In this paper, we present information about genomic function and show several methods used in functional research.


Keywords: genomic function analysis methods


Corresponding author: E-mail: [email protected]

Article Details

Section
Review Ariticle

References

[1] Adams, M.D., J. M. Kelley et al., Complementary DNA sequencing: Expressed sequence tags and human genome project, Science, 252, 1991, 1651-1656.
[2] Adams, M.D., M. Dubnick, A. R. Kerlanage, et al., Sequence identification of 2,375 human brain genes, Nature, 355, 1992, 632-634.
[3] Aharoni, A., O. Vorst, DNA microarrays for functional plant genomics. Plant Mol. Biol., 48(1-2), 2002, 99-118.
[4] Bailey, J. E., Lessons from metabolic engineering for functional genomics and drug discovery, Nat. Biotechnol., 17, 1999, 616-618.
[5] Blocker, H., Genome research and molecular biotechnology, Journal of Biotechnology, 41, 1995.
[6] Boguski, M.S., C. M. Tolstoshev, and D. E. Bassett Jr., Gene discovery in dbEST, Science, 265, 1994.
[7] Bond, U., S.G.Campbell et al., A model organism for genomic and postgenomic studies, Engineering in medicine and biology, 7-8, 2001, 22-32.
[8] Brett, D., J. Hanke, et al., EST comparison indicates 38% of human mRNA’s contain possible alternative splice forms, FEBS Lett., 474, 2000, 83-86.
[9] Brown, M.P., W.N. Grundy, D. Lin et al., Knowledge-based analysis of microarray gene expression data by using support vector machines, Proc. Nat. Acad. Sci. USA, 97, 2001, 262-267.
[10] Chen, T., X. R. Liao, J. F. Du, et al., The anvancement of functional genomics research, Biotechnology Bulletin, 2, 2000, 1-6.
[11] Dalevi, D. and S.G.E. Anderson, Discovering the dynamics of microbial genomes, Engineering in Medicine and Biology, July/August, 2001, 55-60.
[12] Eisen, M.B., P. T. Spellman, P. O. Brown, and D. Botstein, Cluster analysis and display of genome-wide expression patterns, Proc. Nat. Acad. Sci. USA, 95, 1998, 14863-14868.
[13] Gatto, J.G., The changing face of bioinformatics, Drug Discov Today, 8(9), 2003, 375-376.
[14] Gautheret, D., O. Poirot, F. Lopez, S Audic, and J. M. Claverie, Alternate polyadenylation in human mRNAs: A large-scale analysis by EST clustering, Genome Res., 8(5), 1998, 524-530.
[15] Gavin, A. C. et al., Functional organization of the yeast proteome by systematic analysis of protein complexes, Nature, 415, 2002, 141-147.
[16] Golub, T.R., D. K. Slonim, P. Tamayo et al., Molecular classification of cancer: class discovery and class prediction by gene expression monitoring, Science, 286, 1999, 531-537.
[17] Gombert, A.K., M.M. dos Santos, B. Christensen, and J. Nielsen, J., Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae at different conditions of glucose repression. J. Bacteriol. 183, 2001, 1441-1451.
[18] Guyon, I., J. Weston, S. Barnhill, and V. Vapnik, Gene selection for cancer classification using support vector machines, Machine Learning, 46, 2002, 389-422.
[19] Hillier, L., N. Clark, T. Dubuque, et al., Generation and analysis of 280000 human expressed sequence tags, Genome Res., 6, 1996, 807-828.
[20] Ito, T., T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki, A comprehensive two-hybrid analysis to explore the yeast protein interactome, in Proc. Nat. Acad. Sci. USA, 98, 2001, 4569-4574.
[21] Iyer, V.R., C.R. Horak, et al., Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature, 409, 2001, 533-538.
[22] Kan, Z., E. C. Rouchka, W. R. Gish, and D. J. States, Gene structure prediction and alternative splicing analysis using genomically aligned EST’s, Genome Res., 11, 2001, 889-900.
[23] Lan, N., J. Ronald et al., Toward a systematic definition of protein function that scales to the genome level: defining function in terms of interactions, Progressings of the IEEE, 90(12), 2002, 1848-1857.
[24] Li, M. F., and S.Y. Eun, Improving Reliability of Gene Selection From Microarray Functional Genomics Data, Transactions on Information Technology in Biomedicine, 7(3), 2003, 191-196.
[25] Liu, M., Y. Cao, Y. Jiang, Large scale functional genetics analysis with RNAi, Chinese Bulletin of Botany, 2002, 19(4), 491-495.
[26] Maaheimo, H., J. Fiaux, Z.P. Cakar et al., Central carbon metabolism of Saccharomyces cerevisiae explored by biosynthetic fractional 13C labeling of common amino acids. Eur. J. Biochem. 268, 2001, 2464-2479.
[27] MacBeath, G., and S. L. Schreiber, Printing proteins as microarrays for high throughput function determination, Science, 289, 2000, 1760-1762.
[28] Madden, S.L., C.J. Wang, and G. Landes, Serial analysis of gene expression: from gene discovery to target identification, Drug Discovery Today, 5(9), 2000, 415-425.
[29] Mironov, A. A., J. W. Fickett and M. S. Gelfand, Frequent alternative splicing of human genes, Genome Res., 9, 1999, 1288-1293.
[30] Nielsen, J. et al., An expanded role for microbial physiology in metabolic engineering and functional genomics : moving towards systems biology, FEMS Yeast Research, 2(2), 2002, 175-181.
[31] Okubo, K., H. Hori, et al., A novel system for large-scale sequencing of cDNA by PCR amplification, DNA Sequence, 2, 1991, 137-144.
[32] Raamsdonk, L.M. et al. A functional genomic strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat. Biotechnol. 19, 2001, 45-50.
[33] Roessner, U., C. Wagner, J. Kopka et al., Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J. 23, 2000, 131-142.
[34] Schwikowski, B., P. Uetz, and S. Fields, A network of protein – protein interactions in yeast, Nature Biotechnol., 18, 2000, 1257-1261.
[35] Shatkay, H., E. Stepthen, B. Mark, Information retrieval meets gene analysis, Intelligent system in biology, March/April, 2000, 45-53.
[36] Staab, S., Mining Information for Functional Genomics, IEEE Intelligent systems, May/July, 2002, 66-80.
[37] Tamayo, P., D. Slonim, J. Mesirov et al., Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation, Proc. Nat. Acad. Sci. USA, 96, 1999, 2907-2912.
[38] Uetz, P. et al., A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 2000, 623-627.
[39] Uetz, P. et al., A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 2000, 623-627.
[40] Vasmatzis, G., M. Essand, et al., Discovery of three genes specifically expressed in human prostate by expressed sequence tag database analysis, Proc. Nat. Acad. Sci., 95, 1998, 300-304.
[41] Wang, Z., Z.Z. Mei, Z.X. Sun et al., Antisense nucleic acid-the valuable tool of study genomic function, Foreign Medicine-Genetics, 25(1), 2002, 1-3.
[42] Whitchurch, A.K., Gene expression microarrays, Protentials, Feb./Mar., 2002, 30-34.
[43] Wiechert, W., 13C Metabolic flux analysis. Metab. Eng. 3, 2001, 195-206.
[44] Wolfberg, T.G. and D. Landsman, A comparison of expressed sequence tags (EST’s) to human genomic sequences, Nucleic Acids Res., 25, 1997, 1626-1632.
[45] Yang, Q, J.Z Song et al., A study on biocontrol mechanism of Chaetomium spp, Advanced study on plant pest biological comtrol. Heilongjiang science and technology press, 2000, 110-115.
[46] Yang, Q, L. Mei et al., Methods of transforming resistance gene to benzimidazole funficides into Trichoderma harzianum and Chaetomium globosum, Biological control and bio-technology, Heilongjiang scince and technology press, 2003, 1-8.
[47] Yujie, Chi, Q. Yang, Construction and identification of recombinant plasmid of TUB2 gene and transformation into Chaetomium sp., High Technology Letters, 2, 2003, 34-40.
[48] Zhang, L., W. Zhou, V. E. Velculescu, et al., Gene expression profiles in normal and cancer cells, Science, 276(5316), 1997, 1268-1272.
[49] Zhao, J. H., X. Q. Wang et al., Cotent and methods of functional genomics, Prog. Biochem. Biophys., 27(1), 2000, 6-8.
[50] Zhu, Y.Y., E.M. Michleder, et al., Reverse transcriptase template switching: A SMART approach for full-length cDNA library construction, 30(4), 2001, 892-897.