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Semin Reprod Med 2001; 19(2): 167-174
DOI: 10.1055/s-2001-15396
Copyright © 2001 by Thieme Medical Publishers, Inc., 333 Seventh Avenue, New York, NY 10001, USA. Tel.: +1(212) 584-4662

Differential Hybridization and Other Strategies to Identify Novel Ovarian Genes

Adriano B. Tavares1 2 , Michael S. Esplin1 , Eli Y. Adashi1
  • 1Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Utah Health Sciences Center, Salt Lake City, Utah and
  • 2Department of Obstetrics and Gynecology, School of Medicine of Ribeirao Preto, University of Sao Paulo, Sao Paulo, Brazil
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Publication History

Publication Date:
31 December 2001 (online)

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ABSTRACT

Approaches to define patterns of gene expression have applications in a wide range of biological systems. The completion of the human genome project establishes a unique opportunity to understand the molecular control of different biological events through functional analysis. However, the huge database that currently exists will demand the utilization of high-throughput techniques for the assessment of multiple DNA sequences in a rapid and efficient manner. By determining genes with differential expression, it may be possible to decipher the mechanisms that underlie the control of different physiological pathways, which, in turn, may define future strategies to manage them. Although there exist a vast number of tools to screen genes for differential expression, we briefly examine here only some of those with regard to their advantages and disadvantages.

KEYWORD

Hybridization - microarray - gene - screening

REFERENCES

  • 1 Duguid J R, Dinauer M C. Library subtraction of in vitro cDNA libraries to identify differentially expressed genes in scrapie infection.  Nucleic Acids Res . 1990;  18 2789-2792
    PubMedSearch in Google Scholar
  • 2 Hara E, Kato T, Nakada S, Sekiya S, Oda K. Subtractive cDNA cloning using oligo(dT)30-latex and PCR: isolation of cDNA clones specific to undifferentiated human embryonal carcinoma cells.  Nucleic Acids Res . 1991;  19 7097-7104
    PubMedSearch in Google Scholar
  • 3 Hedrick S M, Cohen D I, Nielsen E A, Davis M M. Isolation of cDNA clones encoding T cell-specific membrane-associated proteins.  Nature . 1984;  308 149-153
    CrossrefPubMedSearch in Google Scholar
  • 4 Sargent T D, Dawid I B. Differential gene expression in the gastrula of Xenopus laevis.  Science . 1983;  222 135-139
    PubMedSearch in Google Scholar
  • 5 Diatchenko L, Lau Y F, Campbell A P. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries.  Proc Natl Acad Sci U S A . 1996;  93 6025-6030
    CrossrefPubMedSearch in Google Scholar
  • 6 Gurskaya N G, Diatchenko L, Chenchik A. Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: cloning of Jurkat cell transcripts induced by phytohemagglutinin and phorbol 12-myristate 13-acetate.  Anal Biochem . 1996;  240 90-97
    CrossrefPubMedSearch in Google Scholar
  • 7 Hennebold J D, Tanaka M, Saito J, Hanson B R, Adashi E Y. Ovary-selective genes I: the generation and characterization of an ovary-selective complementary deoxyribonucleic acid library.  Endocrinology . 2000;  141 2725-2734
    CrossrefPubMedSearch in Google Scholar
  • 8 Lee K F, Kwok K L, Yeung W S. Suppression subtractive hybridization identifies genes expressed in oviduct during mouse preimplantation period.  Biochem Biophys Res Commun . 2000;  277 680-685
    CrossrefPubMedSearch in Google Scholar
  • 9 Kumar T R, Wang Y, Lu N, Matzuk M M. Follicle stimulating hormone is required for ovarian follicle maturation but not male fertility.  Nat Genet . 1997;  15 201-204
    CrossrefPubMedSearch in Google Scholar
  • 10 Dube J L, Wang P, Elvin J, Lyons K M, Celeste A J, Matzuk M M. The bone morphogenetic protein 15 gene is X-linked and expressed in oocytes.  Mol Endocrinol . 1998;  12 1809-1817
    CrossrefPubMedSearch in Google Scholar
  • 11 Liang P, Pardee A B. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction.  Science . 1992;  257 967-971
    PubMedSearch in Google Scholar
  • 12 Sompayrac L, Jane S, Burn T C, Tenen D G, Danna K J. Overcoming limitations of the mRNA differential display technique.  Nucleic Acids Res . 1995;  23 4738-4739
    PubMedSearch in Google Scholar
  • 13 Svanberg B, Ling C, Svensson P A, Johnson M, Carlsson B, Billig H. Isolation of differentially expressed aldose reductase in ovaries after estrogen withdrawal from hypophysectomized diethylstilbestrol treated rats: increased expression during apoptosis.  Mol Cell Endocrinol . 2000;  164 183-190
    CrossrefPubMedSearch in Google Scholar
  • 14 Cowan B D, Hines R S, Brackin M N, Case S T. Temporal and cell-specific gene expression by human endometrium after coculture with trophoblast.  Am J Obstet Gynecol . 1999;  180 806-814
    CrossrefPubMedSearch in Google Scholar
  • 15 Mok S C, Wong K K, Chan R K. Molecular cloning of differentially expressed genes in human epithelial ovarian cancer.  Gynecol Oncol . 1994;  52 247-252
    CrossrefPubMedSearch in Google Scholar
  • 16 von Stein D O, Thies W G, Hofmann M. A high throughput screening for rarely transcribed differentially expressed genes.  Nucleic Acids Res . 1997;  25 2598-2602
    CrossrefPubMedSearch in Google Scholar
  • 17 Sun Y, Hegamyer G, Colburn N H. Molecular cloning of five messenger RNAs differentially expressed in preneoplastic or neoplastic JB6 mouse epidermal cells: one is homologous to human tissue inhibitor of metalloproteinases-3.  Cancer Res . 1994;  54 1139-1144
    PubMedSearch in Google Scholar
  • 18 Hubank M, Schatz D G. Identifying differences in mRNA expression by representational difference analysis of cDNA.  Nucleic Acids Res . 1994;  22 5640-5648
    PubMedSearch in Google Scholar
  • 19 Lisitsyn N, Lisitsyn N, Wigler M. Cloning the differences between two complex genomes.  Science . 1993;  259 946-951
    PubMedSearch in Google Scholar
  • 20 Welford S M, Gregg J, Chen E. Detection of differentially expressed genes in primary tumor tissues using representational differences analysis coupled to microarray hybridization.  Nucleic Acids Res . 1998;  26 3059-3065
    CrossrefPubMedSearch in Google Scholar
  • 21 Chu C C, Paul W E. Fig 1, an interleukin 4-induced mouse B cell gene isolated by cDNA representational difference analysis.  Proc Natl Acad Sci U S A . 1997;  94 2507-2512
    CrossrefPubMedSearch in Google Scholar
  • 22 Bertioli D J, Schlichter U H, Adams M J, Burrows P R, Steinbiss H H, Antoniw J F. An analysis of differential display shows a strong bias towards high copy number mRNAs.  Nucleic Acids Res . 1995;  23 4520-4523
    PubMedSearch in Google Scholar
  • 23 O'Neill M J, Sinclair A H. Isolation of rare transcripts by representational difference analysis.  Nucleic Acids Res . 1997;  25 2681-2682
    CrossrefPubMedSearch in Google Scholar
  • 24 Schena M. Genome analysis with gene expression microarrays.  Bioessays . 1996;  18 427-431
    CrossrefPubMedSearch in Google Scholar
  • 25 Schena M, Shalon D, Davis R W, Brown P O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray.  Science . 1995;  270 467-470
    PubMedSearch in Google Scholar
  • 26 DeRisi J L, Iyer V R, Brown P O. Exploring the metabolic and genetic control of gene expression on a genomic scale.  Science . 1997;  278 680-686
    CrossrefPubMedSearch in Google Scholar
  • 27 Brown M P, Grundy W N, Lin D. Knowledge-based analysis of microarray gene expression data by using support vector machines.  Proc Natl Acad Sci U S A . 2000;  97 262-267
    CrossrefPubMedSearch in Google Scholar
  • 28 Hayward R E, Derisi J L, Alfadhli S, Kaslow D C, Brown P O, Rathod P K. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria.  Mol Microbiol . 2000;  35 6-14
    CrossrefPubMedSearch in Google Scholar
  • 29 Lashkari D A, DeRisi J L, McCusker J H. Yeast microarrays for genome wide parallel genetic and gene expression analysis.  Proc Natl Acad Sci U S A . 1997;  94 13057-13062
    CrossrefPubMedSearch in Google Scholar
  • 30 Wikman F P, Lu M L, Thykjaer T. Evaluation of the performance of a p53 sequencing microarray chip using 140 previously sequenced bladder tumor samples.  Clin Chem . 2000;  46 1555-1561
    PubMedSearch in Google Scholar
  • 31 Alon U, Barkai N, Notterman D A. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays.  Proc Natl Acad Sci U S A . 1999;  96 6745-6750
    CrossrefPubMedSearch in Google Scholar
  • 32 Schummer M, Ng W V, Bumgarner R E. Comparative hybridization of an array of 21,500 ovarian cDNAs for the discovery of genes overexpressed in ovarian carcinomas.  Gene . 1999;  238 375-385
    CrossrefPubMedSearch in Google Scholar
  • 33 DeRisi J, Penland L, Brown P O. Use of a cDNA microarray to analyse gene expression patterns in human cancer.  Nat Genet . 1996;  14 457-460
    PubMedSearch in Google Scholar
  • 34 Iyer V R, Eisen M B, Ross D T. The transcriptional program in the response of human fibroblasts to serum.  Science . 1999;  283 83-87
    CrossrefPubMedSearch in Google Scholar
  • 35 Heller R A, Schena M, Chai A. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays.  Proc Natl Acad Sci U S A . 1997;  94 2150-2155
    CrossrefPubMedSearch in Google Scholar
  • 36 Hegde P, Qi R, Abernathy K. A concise guide to cDNA microarray analysis.  Biotechniques . 2000;  29 548, 554-556 558-560
    PubMedSearch in Google Scholar
  • 37 Lockhart D J, Winzeler E A. Genomics, gene expression and DNA arrays.  Nature . 2000;  405 827-836
    CrossrefPubMedSearch in Google Scholar
  • 38 Lee M L, Kuo F C, Whitmore G A, Sklar J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations.  Proc Natl Acad Sci U S A . 2000;  97 9834-9839
    CrossrefPubMedSearch in Google Scholar
  • 39 Eisen M B, Spellman P T, Brown P O, Botstein D. Cluster analysis and display of genome-wide expression patterns.  Proc Natl Acad Sci U S A . 1998;  95 14863-14868
    CrossrefPubMedSearch in Google Scholar
  • 40 Schena M, Shalon D, Heller R, Chai A, Brown P O, Davis R W. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.  Proc Natl Acad Sci U S A . 1996;  93 10614-10619
    CrossrefPubMedSearch in Google Scholar