In search of differentially expressed genes and proteins.

A great challenge for modern cell biology is the successful examination of the co-expression of thousands of genes under physiological or pathological conditions and how the expression patterns define the different states of a single cell, tissue or a microorganism. Gene expression can be analyzed today on a large scale by advanced technical approaches for differential screening of proteins and mRNAs. The identification of differentially expressed mRNAs has been successfully applied to understand gene function and the underlying molecular mechanism(-s) of differentiation, development and disease state. Analysis of gene expression by the systematic mapping of thousands of proteins present in a cell or tissue can be achieved by the use of two-dimensional (2D) gel electrophoresis, quantitative computer image analysis, and protein identification techniques. In this article, we comment on some of these techniques and try to stress their advantages and drawbacks. We show how data from RNA/DNA mapping, sequence information from genome projects and protein pattern profiling can be linked with each other and annotated. These comprehensive approaches permit the study of differential gene and protein expressions in cells or tissues.

[1]  Gen Sheng Wu,et al.  Identification op a human hepatocellular carcinoma-associated tumor suppressor gene by differential display polymerase chain reaction , 1995 .

[2]  D. Hochstrasser,et al.  Micropreparative two‐dimensional electrophoresis allowing the separation of samples containing milligram amounts of proteins , 1993, Electrophoresis.

[3]  B. Torok-Storb,et al.  Identification of a novel DNA sequence differentially expressed between normal human CD34+CD38hi and CD34+CD38lo marrow cells. , 1995, Blood.

[4]  R D Appel,et al.  SWISS‐2DPAGE: A database of two‐dimensional gel electrophoresis images , 1993, Electrophoresis.

[5]  J. Reich,et al.  Identification of differentially expressed mRNA species by an improved display technique (DDRT-PCR). , 1993, Nucleic acids research.

[6]  E. Haag,et al.  Effects of primer choice and source of Taq DNA polymerase on the banding patterns of differential display RT-PCR. , 1994, BioTechniques.

[7]  D. Hochstrasser,et al.  Current challenges and future applications for protein maps and post‐translational vector maps in proteome projects , 1996, Electrophoresis.

[8]  S. Douglas,et al.  Use of differential display to identify differentially expressed mRNAs induced by rat carotid artery balloon angioplasty. , 1995, Laboratory investigation; a journal of technical methods and pathology.

[9]  N. Lisitsyn,et al.  Representational difference analysis: finding the differences between genomes. , 1995, Trends in genetics : TIG.

[10]  R D Appel,et al.  Inside SWISS‐2DPAGE database , 1995, Electrophoresis.

[11]  J. Green,et al.  Isolation and characterization of a novel gene expressed in multiple cancers. , 1996, Oncogene.

[12]  P. O’Farrell.  High resolution two-dimensional electrophoresis of proteins. , 1975, The Journal of biological chemistry.

[13]  J R Scherrer,et al.  The MELANIE project: From a biopsy to automatic protein map interpretation by computer , 1991, Electrophoresis.

[14]  A Bairoch,et al.  Two‐dimensional gel electrophoresis of Escherichia coli homogenates: The Escherichia coli SWISS‐2DPAGE database , 1996, Electrophoresis.

[15]  A. Mes-Masson,et al.  Decreased Fas antigen receptor expression in testicular tumor cell lines derived from polyomavirus large T-antigen transgenic mice. , 1996, Oncogene.

[16]  S. Kar,et al.  Differential display and cloning of messenger RNAs from the late phase of rat liver regeneration. , 1995, Biochemical and biophysical research communications.

[17]  O. Hino,et al.  Isolation of Genes Differentially Expressed between the Yoshida Sarcoma and Long‐survival Yoshida Sarcoma Variants: Origin of Yoshida Sarcoma Revisited , 1994, Japanese journal of cancer research : Gann.

[18]  H. Mischak,et al.  Identification of the primary growth response gene, ST2/T1, as a gene whose expression is differentially regulated by different protein kinase C isozymes , 1995, FEBS letters.

[19]  S. Ooi,et al.  Three methods for identification of true positive cloned cDNA fragment in differential display. , 1996, BioTechniques.

[20]  S. Ooi,et al.  New primer strategy improves precision of differential display. , 1995, BioTechniques.

[21]  K. Khanna,et al.  Induction of inositol 1,4,5 trisphosphate receptor genes by ionizing radiation. , 1996, International journal of radiation biology.

[22]  A. Pardee,et al.  Distribution and cloning of eukaryotic mRNAs by means of differential display: refinements and optimization. , 1993, Nucleic acids research.

[23]  J. Celis,et al.  A qualitative and quantitative protein database approach identifies individual and groups of functionally related proteins that are differentially regulated in simian virus 40 (SV40) transformed human keratinocytes: An overview of the functional changes associated with the transformed phenotype , 1994, Electrophoresis.

[24]  L. Huber.  Mapping cells and sub‐cellular organelles on 2‐D gels: ‘new tricks for an old horse’ , 1995, FEBS letters.

[25]  S. M. Saati,et al.  Cataloging altered gene expression in young and senescent cells using enhanced differential display. , 1995, Nucleic acids research.

[26]  M. Wilkins,et al.  Progress with gene‐product mapping of the Mollicutes: Mycoplasma genitalium , 1995, Electrophoresis.

[27]  J. Welsh,et al.  RNA fingerprinting and differential display using arbitrarily primed PCR. , 1995, Trends in genetics : TIG.

[28]  J I Garrels,et al.  A Saccharomyces cerevisiae Internet protein resource now available , 1995, Electrophoresis.

[29]  G. Feuerstein,et al.  Direct sequencing of DNA isolated from mRNA differential display. , 1995, BioTechniques.

[30]  D. Hochstrasser,et al.  A nonlinear wide‐range immobilized pH gradient for two‐dimensional electrophoresis and its definition in a relevant pH scale , 1993, Electrophoresis.

[31]  M Hubank,et al.  Identifying differences in mRNA expression by representational difference analysis of cDNA. , 1994, Nucleic acids research.

[32]  A. Pardee,et al.  Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. , 1992, Science.

[33]  M. Wigler,et al.  Cloning the differences between two complex genomes , 1993, Science.

[34]  K. Kinzler,et al.  Serial Analysis of Gene Expression , 1995, Science.

[35]  T. Jacks,et al.  Identification and cloning of EI24, a gene induced by p53 in etoposide-treated cells. , 1996, Oncogene.

[36]  T. Saheki,et al.  Pancreatic secretory trypsin inhibitor gene is highly expressed in the liver of adult‐onset type II citrullinemia , 1995, FEBS letters.

[37]  P. Liang,et al.  Differential screening of gene expression difference enriched by differential display. , 1996, Nucleic acids research.

[38]  M. Jackson,et al.  Cloning differentially expressed mRNAs , 1996, Nature Biotechnology.