May 2004
Volume 45, Issue 13
ARVO Annual Meeting Abstract  |   May 2004
Functional Classification of Genes Expressed by ARPE–19 Cells
Author Affiliations & Notes
  • D. Johnson
    Ophthalmology, Univ of Tennessee Memphis, Memphis, TN
  • W.E. Orr
    Ophthalmology, Univ of Tennessee Memphis, Memphis, TN
  • A.D. Schmitt
    Ophthalmology, Univ of Tennessee Memphis, Memphis, TN
  • R.K. Sharma
    Ophthalmology, Univ of Tennessee Memphis, Memphis, TN
  • Footnotes
    Commercial Relationships  D. Johnson, None; W.E. Orr, None; A.D. Schmitt, None; R.K. Sharma, None.
  • Footnotes
    Support  NIH Grant EY–13080 and Research to Prevent Blindness
Investigative Ophthalmology & Visual Science May 2004, Vol.45, 1300. doi:
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      D. Johnson, W.E. Orr, A.D. Schmitt, R.K. Sharma; Functional Classification of Genes Expressed by ARPE–19 Cells . Invest. Ophthalmol. Vis. Sci. 2004;45(13):1300.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract: : Purpose: Functional profiling of genes can be useful indicator of the physiological state of cells and how this state changes in response to disease and treatment. Using Affymatrix microarray analysis, we have constructed a functional profile of the genes expressed by the ARPE–19 cell line of retinal pigment epithelium (RPE). This cell line has proven to be a highly suitable culture preparation for detailed studies of RPE function because it retains many RPE–specific phenotypic markers that are absent from other RPE cell lines. Methods: Data collected from four samples of confluent ARPE–19 cell cultures were examined using Arrymatrix software. Results: We have determined that of approximately 19,044 unique gene sequences represented on the HG U133A microarray chip, 6,438 were expressed in ARPE–19 cells irrespective of the substrate they were grown on (plastic, fibronectin, collagen, or Matragel). Rather than focus our subsequent analysis on the identity or level of expression of each individual gene in this large data set, we examined the number of genes expressed within 130 functional categories selected from Affymatrix software search terms. Using this functional classification scheme, we were able to unambiguously categorize about 90% of the expressed genes The resulting ARPE–19 Functional Gene Expression Profile condenses the original data set of over 6,000 data points into a format with 130 data points. When displayed as a percentage of the total number of ARPE–expressed genes, the data can readily be compared with equivalent data from other appropriate samples. For example, comparisons with other cell types would highlight cell–specific attributes of gene expression; comparisons with ARPE cells exposed to other experimental treatments would highlight treatment–induced changes in gene expression. Conclusions: These analyses are based on the assumption that the numbers of genes expressed within a functional category provide a useful indicator of the overall level of activity within that particular functional pathway.

Keywords: gene microarray • gene/expression • gene screening 

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