Appendix 1 of Ruotolo, Mol Vis 2003; 9:538-548.


Appendix 1. List of lens expressed and modulated genes

This appendix includes two files containing separate lists for genes that are expressed in the human lens ("gene-expressed.txt") or modulated in cataractous versus transparent lenses ("gene-modulated.txt").

The file "gene-expressed.txt" contains the list of genes corresponding to spots with "above-background" hybridization signals in transparent human lenses (see the text for details on data analysis). Columns correspond to: (1) GenBank accession number, (2) GenBank gene definition, (3) Gene symbol, (4) flags for "normal lens" hybridization on filter 1 (N1) and for "normal lens" hybridization on filter 2 (N2) as assigned by the Imagene data analysis software (see Methods for details), (5) average of normalized signal intensities obtained from "normal lens" hybridizations conducted on filter 1 and filter 2, and (6) presence in (yes), or absence from (no) lens Expressed Sequence Tag (EST) collections for all hybridization-positive genes identified by our analysis. Flag 0 spots were normalized with respect to the mean of all the hybridization intensities of flag 0 spots. Spots to which a flag 3 was assigned in at least one hybridization were normalized with respect to the mean intensity of all "above-background" spots.

The file "gene-modulated.txt" contains the list of genes that are differentially expressed in transparent versus nuclear cataractous lenses (see the text for details on data analysis). Columns correspond to: (1) GenBank accession number, (2) GenBank gene definition, (3) Gene symbol, (4) flags for "normal lens" hybridization on filter 1 (N1) and for "normal lens" hybridization on filter 2 (N2) as assigned by the Imagene data analysis software (see Methods for details), (5) flags for "cataractous lens" hybridization on filter 1 (C1) and for "cataractous lens" hybridization on filter 2 (C2) as assigned by the Imagene data analysis software, and (6) ratio between the average of normalized signal intensities for "normal lens" hybridizations (IN) and the average of normalized signal intensities for "cataractous lens" hybridizations (IC). Flag 0 spots were normalized with respect to the mean of all the hybridization intensities of flag 0 spots. Spots to which a flag 3 was assigned in at least one hybridization were normalized with respect to the mean intensity of all "above-background" spots.

To access this data, click or select the words "normalized data". This will initiate the download of a compressed (zip) archive. This file should be uncompressed with an appropriate program (the particular program will depend on your operating system). Once extracted, you will have a folder (or directory) containing two files. The files are tab delimited text. Most spreadsheet programs will import files in this format.


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