Appendix 1. Raw affymetrix chip data with EASE analysis

These files are the raw affymetrix data and the entire EASE data analysis. The file entitled "raw-data.txt" is a list of all of the genes that are either increased or decreased by 2 fold or greater levels according to the affymetrix chip data. The list includes each gene's relative signal intensity, statistical probability, and description. The file entitled "increased-2-fold.txt" represents the EASE analysis data for all of the genes that are increased by 2 fold or greater levels according to the microarray data with the statistical analysis for each of the categories. This is the data that was used to create Figure 5 and Figure 6. The file entitled "decreased-2-fold.txt" represents the EASE analysis data for all of the genes that are decreased by 2 fold or greater levels according to the microarray data with the statistical analysis for each of the categories. This is the data that was used to create Figure 7 and Figure 8. The file entitled "scatter-plot.jpg" is a graphical representation of the expression differences between cataract and clear lenses. The Y-axis is the signal intensity value of the clear lens hybridization versus the cataract hybridization. The X-axis is the cataract signal intensity value. Each dot on this graph represents an individual gene. The blue dots are genes increased in cataract while the red dots represent genes decreased in cataract. The green lines indicate fold-chage values with the two most exterior lines representing 10 fold and the two most interior lines represent 2 fold changes. The middle lines represent 3 fold changes.

To access this data, click or select the words "data and analysis". 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 eight files (one for each microarray). The files are tab delimited text. Most spreadsheet programs will import files in this format.